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Web-Ice Manual - Macromolecular Crystallography

1. Port A3 CrystalID A3 Protein nyo Comment nyoglobin sucrose cryo SystemWarning Directory null FreezingCond a CrystalCond Metal Priority Person CrystalURL ProteinURL Figure 26 Sample editing tool 5 1 6 Sorting samples Some column headers are displayed as links Clicking on will result in column sorting toggled between ascending and descending For example to sort the samples by score click on the Score column header Note The sorting affects the table display only The actual Excel spreadsheet is always sorted by port ID unless the user edits the Excel file directly 5 1 7 Updating the Spreadsheet The spreadsheet is updated with the latest available screening results automatically every 5 seconds by default this can be changed from the Preferences Tab see section Z 5 4 The Update button can also be used to reload the spreadsheet from the crystals server 5 2 Cassette Details The Details page is similar to the Image Viewer tab but instead of using the file browser to locate the image file the user uses the cassette browser The top left frame displays one of the images of the selected crystal Like in the Image Viewer the user can zoom pan and adjust the brightness The Analyze Image button displays the image with highlighted spots picked by SPOTFINDER The user can toggle between Analyze Image and Image Only to display or hide the highlighted spots The top right frame contains various tabs that dis
2. output files and full logs from the processing job stored under the data user webice process DatasetName di rectory There is a subdirectory per program except for XDS in which two different directories xds1 and xds2 are used to store the autoindexing and the integration files and a third directory xds contains the results from both stages Other directories less interest ing to the user are the scratch directory which contains intermediate output files plots containing the data displayed in the browser Plots page and metadata with input and results related to Restflow 4 5 Reprocessing the data The command files written to the webice process subdirectory can used for reprocessing the data set with different input parameters If you are not familiar with the programs used for processing consult the documentation available online in the software paged or consult with the beamline support person http smb slac stanford edu facilities software 36 5 Screening Crystals The Screening tab provides an interface to view the results of automated screening with the Blu Ice DCS software The screening tab allows viewing and editing of the spread sheet containing sample information and diffraction analysis results and also detailed in spection of the images and results obtained for each screened sample When clicking on the Screening Tab for the first time in the session the browser dis plays the User Cassettes
3. 2007 12 54 26 PM note screening rees start data rees 22 Jun 2007 12 54 26 PM note screening cassette SSRLO70622 SSRL00147 blue xis rees SS 22 Jun 2007 12 54 26 PM note screening detector_z 350 000 mm 22 Jun 2007 12 54 26 PM note screening beam size 0 200 X 0 200 mm 22 Jun 2007 12 54 26 PM note screening energy 12657 974 ev 22 Jun 2007 12 54 26 PM note screening attenuation 0 000 22 Jun 2007 12 54 26 PM note screening beamstop_z 40 005 mm 22 Jun 2007 12 54 26 PM note screening dose mode off 22 Jun 2007 12 56 25 PM note screening 22 Jun 2007 12 58 56 PM note screening ees start data rees 22 Jun 2007 12 58 56 PM note screening cassette SSRL0O70622 SSRL00147 blue xls rees S 22 Jun 2007 01 02 05 PM note screening 22 Jun 2007 01 03 27 PM note screening Figure 29 Beamline Log page Clicking on the Download button at the top of the log will open a separate browser win dow containing only the log which can then be saved as a file in the user s disk area The 44 New Log button clears the contents of the log 7 Preferences The Preference tab can be used by the user to edit several options affecting how and when the data are displayed by Web Ice 7 1 Saving the Preferences The values entered by the user in the Configuration table will be valid the first time the user visits the different Web Ice tools If t
4. 73 Ta 174 W 75 Re 76 Os 77 Ir 78 Pt 79 Au lso Hg 81 TI 82 Pb 183 Bi 84 Po 85 At 86 Rn Li Li Li Li Ll Li jul Li Li L2 L2 L2 L2 L2 L2 12 L2 L2 L2 L3 L3 L3 L3 L3 L3 L3 L3 E L3 IL3 L3 87 Fr 88 Ra 89 Ac 58 Ce 59 Pr 60 Nd 61 Pm 62 Sm 63 Eu 64 Gd 65 Tb 66 Dy 67 Ho 68 Er 69 Tm 70 Yb 71 Lu Li ui fea fut fer fei feri fei ai i ju L2 L2 fre fr fi fi fee fr fr fr e lis fis e e e e je bo Th 91 Pa 92 U Figure 10 Selection of absorption edge to do a fluorescence scan specifying the full path name in the input text box next to the Load Scan File button Note only the peak energy is required for a SAD experiment To do a two wavelength MAD experiment change one of the energy input boxes to O it is best to leave out the peak or the inflection energy the remote energy should always be collected on MAD experiments Note If a fluorescence scan is not collected and summary file is not given it is recommended to supply the heavy atom type This makes it possible to give a more accurate estimate of the radiation dose for the experiment Choose other options fig The user can choose the exposure time oscillation angle beam attenuation and resolution for the test images The default exposure time is a reasonable value for well diffracting crystals at the selected beamline The default resolution is based on the current detector sample and energy or the absorp
5. Summary page see section 5 1 Note The Update function and button only activate the link to the latest sample for which results are available It does not update the images and results displayed 42 6 Beamline status The beamline tab contains applications to monitor the beamline and experiment status The beamline tab navigation toolbar provides access to the beamline video cameras data collection status and data collection log Beamline Selections Video Status Log Figure 27 Navigation toolbar in the Beamline tab 6 1 Beamline Selection This page is used to select a beamline The functionality is identical to that of the Beam line drop down menu fig T in the navigation toolbar 6 2 Beamline Video The Video link in the beamline navigation toolbar opens a page displaying almost real time video streams of the sample and beamline equipment Two pan tilt zoom cameras inside the beamline hutch the hutch camera and the robot camera provide views of experimental hardware A pan tilt zoom camera outside the hutch the control panel camera provides views of the instrument console and electronics systems Each video feed can be displayed separately by clicking on the corresponding camera link in the navigation toolbar This can be useful when Web Ice is accessed through a slow Internet connection The refresh rate for the video can also be adjusted in the Preferences Tab see section 7 6 For a list and description of ava
6. a list of the spreadsheets fig 23 previously uploaded to SSRL by the user When a beamline is selected figl the Beamline Cassettes will list the spreadsheets currently assigned to each cassette position in the beamline The search tool at the top makes it easy to locate a specific spreadsheet The search input box allows use of the wild card in this case all the spreadsheets matching the partial name will be displayed The spreadsheet contents are accessed by clicking on one of the following links e Summary Displays the selected spreadsheet in a table format It also allows access to a tool to edit the spreadsheet contents e Details Allows detailed inspection of the diffraction image analysis and autoindex results for each sample e Download Excel Allows the user to download the spreadsheet to the user s com puter If the spreadsheet has been used in the automatic screening the image anal ysis and autoindexing results will be in the spreadsheet The link Upload new spreadsheet directs to the Screening System Database usually to upload a new spreadsheet User Cassettes BL1 5 Cassettes Cassette Summary Cassette Details Find Uploaded Spreadsheet Y 2006 Search SILID Uploaded Spreadsheet Upload Time Commands 4967 SMB_Oct_2006 xIs 2006 11 01 15 58 45 Summary Details Download Results Delete 5067 SMB_Oct_2006 x1s 2006 11 10 11 06 06 Summary Details Download Results Delete 5088 SMB_Nov16_2006
7. an appropriate value before hand The option to collect images and autoindex can be selected from the New Run form fig 6 after choosing an accessible beamline from the toolbar Creating the run will take the user to the Setup pages The Prev and Next buttons can be used to navigate between the following steps 1 Choose sample In the current version of Web Ice the user may only collect images from samples which have been already mounted either by the robot via Blu Ice or manually In later releases it will be possible to use the robot to mount samples from Web Ice 2 Choose Directory and image root name The directory where the test images will be written to can be typed in or if it already exists selected using the Browse tool The image root name will default to the run name 3 Choosing the strategy The user has the option to select the strategy using beamline specific parameters this option takes into consideration the detector position and energy limits enabled at the beamline and uses the beam intensity to provide an estimate of the absorbed dose The option not to calculate the strategy is useful if the user does not intend to collect data from the crystal but only examine the diffraction quality e g during manual sample screening 4 Choose the type of experiment see section 3 2 1 For SAD and MAD experiments there is the option to collect a fluorescence scan from the anomalous element of interest to do this sele
8. buttons or by entering a zoom level in the zoom text box When the image is zoomed out to the maximum the zoom is level is 1 0 it can not go lower than this The higher the zoom level the more zoomed in the image The left arrow button is for zooming out and the right is for zooming in 2 3 3 Adjusting Brightness Brightness of the image is controlled by the Brightness buttons and text box below the zoom buttons The left arrow button makes the image darker and the right button makes it lighter The brightness range is usually between 100 2000 The lower the number the darker the image Brightness of 200 500 is typically good for most images 2 3 4 Changing Size By default the image size is 400 by 400 pixels The user can change the image display size by selecting a different size from the drop down menu located under the brightness buttons 2 4 Image header The image header is retrieved via the image server The header Table T displays useful information about the image 2 5 Analyzing the image When the user clicks on Analyze Image Web Ice will run LABELIT SPOTFINDER module to analyze the image The results of the analysis will be displayed under Spot Statistics in the right hand side frame of the Image Viewer page Alternatively the user can choose to perform image analysis automatically for each image selected by setting this option in the Preferences Tab see section 7 3 When the image has been analyzed the user can use
9. initial estimate for the mosaicity based on how many of the observed spots are predicted by the best solution and a list of index ing solutions For each indexing solution the programs displays the following e Metric fit This is a measure of the distortion of the unit cell required to fit the symmetry This increases with the symmetry but often remains below 0 1 for good solutions e rmsd Root mean square deviation between the observed and the predicted pattern Usually less than 0 5 for good cases e spots Number of spots predicted by the solution up to a maximum of 600 e Crystal system Unit Cell in A Volume cell volume 26 3 4 4 Solution A summary of the refinement and integration results for the indexing solution determined by LABELIT is shown at the top of the page Note that for strong diffraction images the estimated resolution limit may extend well beyond the limits of the detector in order to collect data to this resolution you should then move the detector closer to the sample changing the exposure time by a large amount may have an effect on this estimate Note be aware that the estimated mosaicity value can be underes timated for well diffracting crystals The estimated value treated as suspect until several contiguous images are available for postrefine ment The profile fitting for the central region of the images and intensity integration statistics are displayed below the Integrated Solut
10. p3 P312 P321 P6 P622 1 28 A A2_004 img 0 mm myoglobin sucrose 90 00 120 00 eryo Figure 24 Cassette Summary the users spreadsheet is displayed in table format 5 1 1 Screening Results If the user collects two images during screening autoindexing of the images will be car ried out automatically The following columns will be shown in the Cassette Summary Results view and appended to the user s spreadsheet e Unit cell and Bravais lattice Note that the symmetry is at this point just an ed ucated guess The actual Laue group and the presence of pseudo symmetry can only be detected during scaling Sometimes particularly if the diffraction is poor a lower symmetry than the correct one can be chosen by LABELI 3 e Mosaicity The initial mosaicity estimate by MOSFLM The estimate is based on how many observed spots are predicted and it is good enough for strategy calcu lation and sample characterization A more accurate value can be obtained after post refinement using a larger number of images http adder Ib1 gov labeli 38 e Rmsr Root mean square deviation between the observed and predicted spots as calculated by MOSFLM after image integration It is usually around 0 05 or less for good crystals e Resolution The diffraction limit of the crystal at the used exposure time based on the 1 01 values The limit is set at J oJ 1 5 If the diffraction is very strong the resolution may extend beyond the limit set by the det
11. server Let the user support person know about this Q When I try to collect images or export a run to Blu Ice I get an error message saying that there are too many runs already What does this mean There is a maximum limit of 16 data collection runs in Blu Ice When all the runs have been used up Web Ice will give this error message If this happens open a Blu Ice window via the NX client if you are a remote user and delete some runs manually doing this will NOT delete or affect the data collected by these runs 49 Q When I change the oscillation angle before Exporting the run to Blu Ice the exposure time changes when I recalculate the dose The exposure time should be proportional to the oscillation angle some people forget to adjust the former when modifying the latter that s why the software will change it How ever if you really do intend to change the exposure per degree just edit the exposure time After that you will be able to change the oscillation angle without automated corrections of the exposure time Q Autoindex Screening fails with a MOSFLM error What has hap pened After autoindexing the images LABELIT runs MOSFLM to integrate the images This serves to confirm that the lattice chosen by LABELIT is correct and provides additional information about the crystal diffraction properties and qualities Unfortunately the inte gration step sometimes fails particularly for poor crystals If this happens yo
12. to maximize anomalous pairs has been en abled in the strategy page Autoindex Tab 9 Video monitoring of the beamline available from the Video Tab 10 Improved strategy calculation using BEST and RADDOSE 11 Possibility to export the strategy to Blu Ice DCS 12 Updates for LABELIT and SPOTFINDER result in a more robust autoindexing 2 Image Viewer The Image Viewer is used to view and analyze diffraction images located on the file server at SSRL The image files are subject to the Unix security restrictions The user must have a read permission to the image file in order to load and view the image The viewer comprises three frames fig The left frames displays a JPEG of the se lected diffraction image The file path of the displayed image file is shown above the JPEG image Next to the image there is a control panel for adjusting the image display parameters such as zooming and panning The right frame displays either the selected image header or when images analysis is requested the analysis results The bottom frame is a file browser that allows the user to select an image file and explore directories The starting search directory will be the one set in the Preferences tab see section 7 3 2 1 Selecting an Image File Image files must be in the MC file system and be readable by the user There are three ways to select an image to be displayed 1 Type in an image name full file path in the text box below the image d
13. 006 13 07 30 B2summary rwxr 212 11 02 2006 18 24 23 Figure 8 Selection of MAD experiments type for Autoindex Only option For MAD and SAD experiments the energies may be input by the user or imported from an autochooch summary file use the directory browser tool to locate the sum mary file select 1t by clicking on the radio button next to the file name and then click on the Load Scan File button Important The File filter in the Preferences 19 tab see section 7 must contain the entry summary for the directory browsing tool to display this file type To do atwo wavelength MAD experiment change the appropriate energy input box to 0 it is best to leave out the peak or the inflection energy the remote energy should always be collected on MAD experiments It is also possible to enter the file name specifying the full path name in the input text box next to the Load Scan File button Note that only the peak energy needs to be entered for a SAD experiment The element and edge input boxes will be read in from the summary file Note If a summary file is not given it is recommended to supply the heavy atom type This makes it possible to give a more accurate estimate of the radiation dose for the experiment Other options fig 9 The user can select the Laue group and cell if known If given the program will calculate the strategy only for that space group If not given the strategy will be
14. 42 adprocOI slac stanford edu Delete 6 03 11 04 05 13 39 22 YI6ADI03A b5_4_0001 img not running 8381 adproc02 slac stanford edu Delete Y I6ADI103A a 11 04 05 13 42 30 YI6AD103A bS_4_0001 img not running 25488 adprocO1 slac stanford edu Delete Y32FM116A 11 04 05 13 29 54 y32am116a_10_0001 img not running 29300 adproc02 slac stanford edu Delete Y32FYS7A 11 04 05 13 24 55 y32fy57a_11_0001 img not running 12555 adprocOl slac stanford edu Delete Figure 18 Process tab page showing a summary of all processed datasets The processing run results can be browsed by clicking on the Dataset Name of interest The runs can be sorted by ascending or descending alphabetical order or by the time of creation The Update reloads the page and displays any new results generated since the last visit to the page Once data processing has been started the run parameters cannot be modified In order to change processing parameters a new run must be started from scratch 4 2 Starting a processing run Clicking on the New Dataset link in the Process navigation toolbar open the data pro cessing input form fig 19 If a form has been filled in previously for another run the form will be pre populated with the same values e The Dataset Name is a compulsory field The name must be a single word of alphanumeric characters and it must be unique a name used for another processing run will be rejecte
15. Contents 1_ Getting Started 1 1 Web Ice September 23 2015 A brief introduction to Web Icg A e s e na e A ee we SS we OES 5 8 du deuce da did kee Go da 1 2 1 Supported browsers a gk wae e ES OM eh a eee ee ee ee nr Jew meen Ale PAM Aang ae mg L51 3015 153 2013 15 5 2011 1 5 6 2010 1 5 8 2008 1 5 9 2007 21 Selecting an Image Filg 2 1 1 Displaying the last image collected 11 ee ee 12 a bbe eee 12 rd iaa 12 Ia ee osos a 12 A 13 do ere 13 ss a 13 a 13 A o daa ea 13 3_ Autoindex and strategy calculatio 16 3 1 The Runs Paga s s ssa a Sa e dd a o a P A 16 3 1 1 Selecting arun o ooa 17 3 1 2 Deleting rung onana a a 17 AA 17 18 21 23 3 2 4 Importing the screening strategy 24 Pep bee eee be thee hoe eed aes 25 CAM ca o AA 25 ORI Tee eee ee ee Tre 25 BAM Scan sear poss ta e Xa a Se cr AS 26 E A a a ae eh Gos a E E S eet Ge Pe S 26 3 4 3 _Autoindex Summary aooo aa a a a a a 000408 26 3 4 4 Solution oaa a a 27 SAA e srepet a an as eee e a oe 27 34 6 Deta u bed eck ate Hh we EAE a we A ee a ee 27 347 Strateoy ses aerate anida ee RE HS 28 3 5 Initiating data collection 2 2 00 004 bee 31 32 ML RUDS gos p lt rrt BSE RSE BPE RSE RESETS BSR E ES 33 ee eee ee eee ee 33 ee ee ee ee ee 34 ibe oe pees oe Bes oes ee eS a 35 441 Da 35 4 4 2 Summa
16. calculated for the lowest space group belonging to the predicted Bravais lattice For SAD and MAD experiments it is possible to enter the number of residues and heavy atoms in the monomer If given and the atom type is known they will be used in the dose calculation for the strategy and also the exposure time and total number of images based on the estimated signal The page also displays the program used to calculate the starting and total rotation angle BEST is used to calculate the full oscillation range for data collection for multicrystal data collection MOSFLM is used instead Choose Dir and Images gt gt Choose Strategy Options gt gt Choose Experiment gt gt Choose Oth Choose Other Options Prev Next Autoindex Options Multicrystal experiment O Yes ONo Select Yes if this run is part of an experiment involving multiple crystals Strategy Program BEST gt Laue group P4 gt Compulsory for multicrystal experiments Unit cell a 0 0 b 0 0 c 0 0 cc 0 0 p 0 0 y 0 0 Cell parameters are optional but if given a Laue group must also be specified Figure 9 Symmetry and strategy options 20 3 2 2 Collecting test images and autoindexing This option allow the user to collect test images and a fluorescence scan from a sample In the current version the sample must be previously mounted by hand or using the robot via Blu Ice and centered by the user The slit size should also be set to
17. chosen and the Mn 1 sd I in the highest reso lution bin is smaller than the specified I Sigma the approximate resolution is calcu lated based on the desired cutoff and the higher resolution shells are omitted from subsequent data processing e If the model is given it will be used to search for a solution by molecular replace ment 4 3 Running data processing Once the dataset form have been filled up processing is initiated by clicking on the Create Run button The browser will display the results page fig 20 which shows the status of the job and links to summarized results and plots by all the different programs 34 ana Datasets New Dataset Selected Dataset Beumline Select beamline SecondMutant Setup Logs Summary Plots Details Update First Image ml 16a a8_8_0001 img Last Image m1 16a a8_8_0720 img Resolution 1 8 Model data ana JASON M1 16A d40n pdb Mean D sd D 0 0 16 10 57 Running XDS DEFPIX INTEGRATE CORRECT 2 b Qp Abort Figure 20 Results page page during run time 4 4 Processing results 4 4 1 Logs The Logs page links to a time stamped log fig21 listing the programs that have been run and in some cases an extract of the results The Log can be refreshed while the processing is running by clicking on the Update Log button The Error Log lists fatal errors during execution of a program or script It can be useful to trace the ultimate cause of a problem d
18. ct the Perform Fluorescence scan option and click on the absorption edge of interest in the periodic table appearing at the bottom of the page fig 110 For SAD experiments the periodic table will enable selection of elements with out an absorption edge in the beamline spectral range Clicking on the element name will select the lowest energy attainable at the beamline for maximizing the anomalous signal present in the data Important This choice of energy does not guarantee that the anomalous signal can be detected In some cases collecting high redundancy data will also be necessary in the current version this can only be done by manually extending the phi range supplied by Web Ice If the option to collect the scan is not used the energies may be input by the user or imported from an autochooch summary file fig 8 use the directory browser tool to locate the summary file select it by clicking on the radio button next to the file name and then click on the Load Scan File button You can also enter the file name 21 Periodic Table 1H 2 He 3Li 4 Be SB j6C h N 80 9F 10Ne 11 Na 12 Mg 13 Al 14 Si ISP _ 16S 17C1 18 Ar 19 K 20 Ca 21 Se 22 Ti 23 V 24 Cr 25 Mn 26 Fe 27 Co 28 Ni 29 Cu 130 Zn 31 Gal32 Ge 133 As 34 Se 35 Br 36 Kr K K K K K K K K K K K 37 Rb 38 Sr 39 Y 40 Zr 41 Nb 42 Mo 43 Te 44 Ru 45 Rh 46 Pd 47 Ag las Cd 49 In 50 Sn 51 Sb 52 Te 531 54 Xe 55 Cs 56 Ba 57 La 72 Hf
19. d 33 ana Datasets New Dataset Selected Dataset Beamline Select beamline New Dataset Form Dataset Name Ist Image data ana JASON M116A m1 16a a8_8_0001 img Browse Last Image optional data ana JASON M116A m1 16a a8_8_0720 img Browse Resolution optional I Sigma optional l Model optional data ana JASON M116A d40n pdb Browse Create Dataset Cancel Figure 19 New run form page e The full path to the first image in the data set must is also a compulsory item The Browse button to the right of the input box can be used for locating the images in the user s data directories e The full path of the last image can also be provided By default all the data with the same root name as the first image will be processed The last image should be given to omit the last images in the data set for example if they show signs of radiation damage or if the are gaps in the rotation the processing script cannot deal with these at the moment e By default all the reflections in the maximum circle inscribed in the detector will be processed To process all the data into the corners of the detector or data con centrated in the middle of the detector enter the appropriate resolution cutoff value in the Resolution input box e The I Sigma box can be used to apply a resolution cutoff based on the Mn I sd 1 value from SCALA If this option is
20. d increase the exposure time 4http smb slac stanford edu facilities software xtal_software raddose htm 33
21. during a screening experiment see section 5 a new run can be created to view the optimal data collection strategy for that sample To do this from the autoindex tab follow these steps 1 Make sure that the appropriate beamline is selected fig T Click on New Run and then on the Import button in the New Run Form page The software will display some information pertaining to the sample A default run name will be built from the spreadsheet ID and the sample name is also supplied 2 Edit the default run name if desired and click Import Run Note It is also possible to import the strategy from the Screening Tab see section 5 1 3 or by launching the Web Ice application from the screening tab in Blu Ice Important The import feature is only enabled if the sample is still mounted on the goniometer If the sample has been dismounted the autoindex must be repeated in order to obtain the optimal phi range for data collection 24 3 3 Executing the run After the run setup has been completed a summary of the user s choices is displayed The user can click the Edit Setup button to change the choices or the Run button to start collecting or autoindexing the images The Run Status will be periodically updated in the Run box fig 13 Messages will be displayed when autoindexing results are ready for viewing It is possible to use other Web Ice tools while the processing is running Clicking the Update button will reload the run content
22. e beam intensity to provide an estimate of the absorbed dose The option not to calculate the strategy is useful if the user does not intend to collect data from the crystal but only examine the diffraction quality e g during manual sample screening 3 Choosing the type of experiment fig 8 The types available are Native MAD three wavelengths and SAD SAD is also the recommended mode to collect data for Isomorphous Replacement phasing Note that two oscillation ranges maximiz ing the unique and anomalous completeness will be always calculated regardless 18 Choose Directory and Images Prev _Next Please choose image directory and images Directory idata btuser BL 9 2 Nov 2006 A2 Browse Imagel A2_8_001 mcca Image2 A2_8_012 meed Figure 7 Selection of directory and images for autoindex of the experiment type The range optimizing anomalous completeness will be se lected by default for MAD and SAD experiments Choose Experiment Type Prev _Next Please choose an experiment type C Native MAD SAD For MAD or SAD experiment Perform Flourescence scan Re use energies from previous scan Please enter energies or select an autochooch summary file from previous scan Inflection fri24 543945 eV Peak f7134 73877 eV Remote fo000 0 eV Scan File data bluser BL9 2 Noy 2006 B2 MAD B2summary Load Scan File data bluser BL9 2 Noy 2006 B2 MAD Up PROCESS drwxr x 4096 11 03 2
23. e maximum resolution in the warning differs noticeably from the other value the values for the exposure time and oscillation angle may not be valid any more In this case it is recommended to recollect test images at the new distance and repeat the strategy calculation e Beamstop Distance Minimum beamstop to sample distance required to collect data at a low resolution of 40 A To collect data at a lower resolution at the expense of a higher image background the beamstop must be moved further back Note that the optimal value is different at wavelengths other than the one used to collect the test images e Energy For native crystal experiments the energy is read from the image header this is also the default for SAD experiments unless the user has selected the element from the periodic table with the Perform Fluorescence Scan option see section 3 2 2 In these cases the software may display a warning suggesting a higher energy for crystals diffracting to very high resolution if so it is recommended to recollect test images with appropriate values of energy and detector distance and repeat the strategy calculation In all other cases the optimal energies for MAD and SAD data collection will be calculated based on a fluorescence scan or values supplied by the user 4Note that the actual attenuation may differ slightly from the calculated attenuation Also on MAD experiments the attenuation at the remote wavelength will be slight
24. e user selected a SAD experiment but clicked on the phi range maximizing unique completeness e Mosaicity and Score These values are shown for information purposes only If the mosaicity is flagged as poor or the score is low it is strongly recommended to inspect the images see section 3 4 5 before proceeding to data collection e Oscillation start and oscillation end For native data collection the default values optimize the unique data completeness For SAD and MAD experiments the values maximizing the anomalous pair com pleteness are selected instead and the total oscillation range is doubled ie the mul tiplicity of the data is doubled for each wavelength since increased multiplicity is better for anomalous signal detection e Oscillation angle The oscillation angle calculated by BEST is used This should not exceed the maximum delta phi value displayed in the strategy summary table e Oscillation wedge For conventional data collection it is suggested to collect the entire run in a single continuous patch For MAD and SAD experiments data collection in wedges is preferable to minimize the amount of damage between Bijvoet or dispersive pairs When feasible the wedge size is chosen so that the total dose received by each wedge of data does not exceed 0 025 MGy However if the dose wedge based size is smaller than a minimum wedge size based on the amount of time needed to change energy on each individual beamline the lat
25. ector area and sample to detector distance used during screening e Score Calculated as 1 0 0 7 x e 4 1 5 x rmsr 0 2 x 1 where d is the resolution limit in A rmsr described above is in mm and ji is the mosaicity in degrees A score of 0 4 0 6 indicates borderline quality Good crystals usually have a score of about 0 8 or higher This score is meant to be used as an initial indicator of the sample quality although it has been found to agree reasonably well with human assessment in many cases it is recommended to inspect the diffraction before choosing a sample for data collection e Image Diffraction image name e System Message If the autoindexing fails the error message from LABELIT will be displayed in this column A second set of results are appended to the Excel file as a separate column for each diffraction image regardless of whether autoindexing has been performed or not In the Cassette Summary page they can be seen by going to the Preferences Tab see section 11 5 and setting the Image Display Type set to Show all Crystal Links for all samples or Show Selected Images only for one sample If a group of two or more contiguous images are collected at each crystal orientation results are given only for the last image in each group These values are particularly useful if the autoindex fails Having an independent qual ity assessment for each image is then useful to determine if the sample meri
26. eriment type if the strategy calculation is not requested 9 For MAD experiments the absorbed dose at each energy is given If the total absorbed dose for three energies exceeds the Garman limit only two energies will be used for data collection 1 5 10 2006 1 Fluorescence scan collection and automated full MAD and SAD strategy calcula tion can be carried out from the Autoindex Tab 2 Beam attenuation is automatically calculated and included in the data collection strategy when the exposure time calculated by BEST is small 3 The resolution limit calculated by LABELIT is used in for image integration This results in fewer autoindex error for low resolution images 4 Automated test image collection implemented in the Autoindex tab 5 The user may supply a specific Laue group and unit cell as input to autoindexing For MAD and SAD experiments it is possible to declare the number of heavy atoms in the molecule This results in a more realistic estimate of the absorbed dose Also the dose is taken into account to calculate a data collection wedge size Autoindex setup page The default data collection strategy is given for this space group 6 The user may configure the image viewer application to perform automated analysis of the image with SPOTFINDER The option is set in the Preferences Tab 7 The crystal score is calculated and displayed when autoindexing using the Autoin dex Tab 8 Selection of a data collection strategy
27. g in using your SSRL computer account name and password You will be di rected to a Welcome page containing a very brief description of the Web interface and instructions to connect to a beamline or obtain on line help The page displayed on log in can be changed by the user see section 7 2 There are also links to Web Ice in the Blu Ice GUI Authentication is not required when logging in through Blu Ice 1 4 Web Ice Interface The Web Ice applications are grouped by function under several menus or Tabs displayed at the top of the Web Ice window By clicking on the tabs the user links to pages provid ing access to the different functions e Image Viewer This tab directs the user to the diffraction image analysis tools interface Here the user can inspect diffraction images and spot statistics e Autoindex This tab provides tools to collect test images optional autoindex calculate a strategy for the experiment and collect a full monochromatic MAD or SAD data set e Process This tab runs a workflow to process analyze scale and merge data and optionally to attempt structure solution by molecular replacement e Screening The Screening tab provides an interface to the the automated screening results Tools to easily identify the best samples for data collection are provided e Beamline Access to different beamline monitoring tools e Video From the video tab the user has access to the beamline video cameras set up to mo
28. he autoindex software best guess of the crystal lattice 6 The estimated diffraction resolution limit based on 01 statistics see section 5 1 1 The runs can be sorted by alphabetical order or by time of creation The Update reloads the page this is useful to display results generated by Web Ice in the background since the last visit to the page 3 1 1 Selecting a run Clicking on a run name allows the user to edit and reuse the run or inspect the results Once a run has been selected it will be highlighted in the user Runs table The user can revisit a selected run by clicking on the name or using the Selected Run link in the navigation toolbar fig 3 1 2 Deleting runs To clear the run and all its contents click the link Delete in the Commands column of the user Runs table 3 2 Generating a new run Selecting New Run link in the Autoindex navigation toolbar opens a new run form page fig 6 The user has three options 1 autoindex existing images stored in the MC com puters 2 import a strategy calculated during screening of the currently mounted sample or 3 to collect and autoindex new test images from a mounted sample The last two op tions require the user to connect to a beamline fig I and they can only be used during beamtime A name for the run must be chosen The run name must be a single word of alphanumeric characters 7 New Run Form Click the Import button to view the strategy generated for the late
29. he user then selects different options while running Web Ice the values in the preferences will be updated To preserve the initial values the user must click the Save button at the bottom of the Configuration Options selection menu 7 2 General Configuration General Configuration al Image Directory data bictl BL9 1 CRYSTAL_CENTER meed img summary Figure 30 General configuration options e Global Image Directory This will be the starting directory to browse the user directories for the input image files e Image Filters Used to specify what files are to be displayed by the directory browser This makes it easier to find types of a certain type Multiples entries separated by a blank space are accepted for example img mccd summary e Show Welcome Page Set to no to stop seeing the Welcome page upon login to the Web Ice interface e Default Tab Select the tab to be displayed upon login to the Web Ice interface 45 Image Viewer Configuration Use Global Image Directory no Imagi data bictl BL9 1 CRYSTAL_CENTER y Show Spot Overlay Automatically Analyze Image yes Figure 31 Image Viewer configuration options 7 3 Image Viewer Configuration e Use Global Image Directory When this is set to Yes the Image Viewer will use the directory specified in the General Configuration see sectio
30. if MOSFLM is used as the Strategy Program and testgen mfm in the solution space group subdirectory and run them as source strategy mfm for example e To recalculate the dose edit the run_raddosel csh file in the solution RADDOSE subdirectory and run RADDOSE by typing source run_raddosel csh Note that for MAD experiments you will also have to run run_raddose2 csh and if using 3 energies run_raddose3 csh to calculate the correct dose at each of the energies used in the experiment See also next question Q My buffer contains 1M NaCl and I have very small crystals How do I account for that in the dose calculation e Open the run_raddosel csh file see previous question Add the line SATM Na 1000 Cl 1000 i e the element s in your sample heavier than oxygen and its concentration in mM e You can also supply the true size of your crystal in the CRYSTAL line the first number should the dimension along the spindle and the number of heavy atoms per monomer under PATM if you have not defined this already using the web interface e Re run RADDOSE as explained in the previous question http www embl hamburg de BEST best3 _manual html 52 See the RADDOSE documentatior 4 Q Why is the predicted resolution lower than I expected If the resolution limit is lower than the target resolution use a longer exposure time for the test images Recollect the test images using the Recollect button an
31. ilable camera preset positions consult the Blu Ice docu mentatio 6 3 Experiment status The Status link in the navigation toolbar directs to a page displaying the data collection status experimental parameters and a thumbnail of the last image collected The image can be inspected in detail by following the link under the image This opens the image in the Image Viewer Tab see section B The status window also indicates whether an experiment is initiated from Blu Ice or Web Ice in the last case the user is allowed to interrupt data collection from the page Beamline Selections Video Status Log Data Collection started by Blulce collect_msg collecing run frame 113 of 360 o osa Run Label 6 i Run Name lea Directory data rees HWP062207 G3 Detector Mode normal Detector Distance 400 0 Beam Stop 30 0 Attenuation i loo Axis Phi Delta los Time j 8 0 Star 12 0 End 192 0 data rees HWP062207 G2 G2_1_112 meed E N Go to Image Viewer edas peng Energy1 112999 0 Energy2 10 0 Energy3 Y 0 0 i a ha Figure 28 Beamline status page 6 4 Experiment log The experiment log page is displayed by clicking the Log link in the navigation toolbar This log is the same one displayed in the Blu Ice log tab Beamline Selections Video Status Log Download Log New Log UserLog data bict1 userLog BL9 2 userLog20070622_113627 ulg 22 Jun
32. ion table To access the entire MOSFLM log and summary file for the integration see the Details link see sectionB 4 6 3 4 5 Predictions To view the predicted spots click on the Prediction tab This page displays the ob served spots and the predicted spots after autoindexing and integration with MOSFLM for either image used for the autoindexing The image display parameters can be modified as described in the Image Viewer documentation see section 2 3 The observed spots used for autoindexing are shadowed in green The predicted spots surrounded by a blue circle are fully recorded The ones surrounded by a yellow circle are partially recorded Ice rings and the initial resolution estimate before autoindexing are also marked 3 4 6 Details Details displays the directory tree containing all the files generated by Web Ice during the autoindex and integration including scripts orientation matrix files logs and output reflection files Access to these files is useful to validate the image analysis results and to refine the strategy calculation by making changes to the input files and re running them manually see section 8 The contents of non binary files can be displayed by clicking on the file name e The top directory in the tree data user id webice autoindex run id contains 27 e The LABELIT subdirectory contains the autoindexing results and the MOSFLM matrix input scripts and output files for each pos
33. irectory Clicking the link for an image file will display the image Note that the user can only browse files and directories that have a read permission for their Unix login id 2 2 Displaying the diffraction resolution Moving the mouse over the diffraction image will display the resolution in the box below the image l File data ana TEST WEBICE T3604 T3604_0_001 i Open Resolution 1 78 A Figure 3 Displaying the resolution at the mouse position in the Image Viewer 2 3 Adjusting Image Display The user can zoom pan adjust brightness and set display size of the image by using the image control panel located to the right of the displayed image 2 3 1 Panning There are three ways to pan the image One is by clicking on the image The image will be moved so that the mouse click position will be come the center of the display The second way to pan the image is by using the thumbnail located at the top of the image control panel When the zoom level is greater than 1 the image is zoomed in the thumbnail displays a red rectangle representing the area of the image being displayed The more the image is zoomed in the smaller the rectangle The user can click anywhere in the thumbnail to move the rectangle 12 The third way to pan the image is by clicking one of the pan buttons which are located below the thumbnail and above the zoom buttons 2 3 2 Zooming The user can zoom the image in and out by using the zoom
34. isplay box in the left frame The file path typically begins with data username or home username for example data joeuser images remo_1_001 img 10 Weblee Welcome Image Viewer Autoindex Screening Beamline Video Preferences Tool Tip Dont see your image files in the file browser Edit File Filters configuration in Preferences General data ana RNASE H8 rnase H8_4_001 img Ls E Zoom Meo El Brightness Wio A Size 300x300 gt Y show spot overlay Analyze Image Last Image File data ana RNASE H8 mase H8_4 X Open Resolution f TRA pe ea Header Spot Statistics Crystal Image OVERLOAD_CUTOFF HEADER_BYTES DIM BYTE_ORDER TYPE SIZE1 SIZE2 PIXEL SIZE BIN DETECTOR_SN TIME DISTANCE PHI OSC_START OSC_RANGE WAVELENGTH BEAM _CENTER_X BEAM _CENTER_Y 1 PIXEL SIZE 0 OSCILLATION RANGE 1 EXPOSURE TIME 2 31 A 1 TWO THETA DETECTOR gt BEAM CENTRE DSC QUANTUM315 57 5 157 5 Help Logout Beamline Select beamline gt a data ana RNASE A3 Update Up rW h16c52 001 img 18874880 01 06 2006 16 52 24 TW chl6c52_002 img 18874880 01 06 2006 16 52 46 Figure 2 Image Viewer 2 The second way to select an image is to use the file browser in the bottom frame as explained below see section 2 1 2 3 The third way is to click on the Prev or the Next buttons located on the right
35. late and set up a data collection strategy in a semi automated fashion the user gets to review and if desired edit the strategy before initiating data collection Web Ice is totally synchronized and can be used simultaneously with Blu Ice 1 1 1 References The main reference to Web Ice is A Gonz lez P Moorhead S E McPhillips J Song K Sharp J R Taylor P D Adams N K Sauter and S M Soltis Web Ice integrated data collection and analysis for macromolecular crystallography J Appl Cryst 41 176 184 2008 External software used by Web Ice include e SPOTFINDER DISTIL diffraction spot location and image analysis Z Zhang H van den Bedem N K Sauter G P Snell and A Deacon J Appl Cryst 39 112 119 2006 e LABELIT autoindexing N K Sauter R W Grosse Kunstleve and P D Adams J Appl Cryst 37 399 409 2004 e MOSFLM data integration and overlap analysis A G W Leslie in Crystallo graphic Computing Oxford University Press 1990 e BEST exposure time calculation and since May 2008 oscillation range A N Popov and G P Bourenkov Acta Cryst D59 1145 1153 2003 e RADDOSE absorbed dose calculation J W Murray E F Garman and R B G Ravelli J Appl Cryst 37 513 522 2004 4 e XDS data processing W Kabsch Acta Cryst D66 125 132 2010 e The CCP4 programs SCALA TRUNCATE MOLREP REFMAC for data process ing scaling analysis structure s
36. lation has not been finished the Update button in the Autoindex Tab to update the contents of the run 5 1 4 Re analyzing samples The Analyze Crystal button can be used to re run the analysis and autoindexing soft ware for a selected sample This is useful if the test images for that sample have been recollected or in case of a software crash or server time out during the first analysis While a sample is being re analyzed the Analyze Crystal button will be disabled Use the Update button see section 5 1 7 to display the new analysis results Typically the crystal orientation will be different after each sample remount so the collection strategy will change accordingly 40 5 1 5 Editing spreadsheet columns To access the sample editing tool select a crystal as described above then click the Edit crystal button at the top of the spreadsheet table This will link to the the Edit crystal tool page shown in figure 26 The selected sample row is displayed and only certain fields are editable Click Set Crystal to save the changes To cancel the changes simply exit the page by clicking the Cassette Summary button to return to the spreadsheet table or All Cassettes or Cassette Details to access the user s spreadsheet list or the detailed screening result viewer respectively Enter comments next to the appropriate field note that some fields are protected When you have finished click on the Set Crystal button Set Crystal
37. ly different to the attenuation at the edge energies 30 e Detector type This is read from the image header and displayed for information purposes e Detector mode Dezingering is suggested for CCD detectors if the exposure time per image is longer than 30 seconds e Inverse beam This option is selected for SAD experiments inverse beam Yes For the other experiment types this is set to No no inverse beam e Number of images Obtained by dividing the total oscillation range by the oscilla tion per image e Absorbed dose Estimate of the absorbed dose assuming no heavy atoms present in the sample a solvent content of 50 and a uniform crystal size of 100 microns For MAD experiments the dose at each energy will be given If the total dose exceeds the Garman limit a warning will be displayed for MAD and SAD experiments a more strict limit half the Garman limit is used as the accurate measurement of anomalous differences is easily affected by radiation damage in addition for MAD experiments only data at two energied will be collected Other measures to reduce the absorbed dose are left to the user s discretion decreasing the exposure time per image is the best option in most cases However if an abundant supply of crystals is available decreasing the number of images is also an option Important The dose calculated for MAD and SAD experiments can be significantly underestimated if the protein buffer cryoprotectant co
38. n tains a high concentration of ions such as Ca Cl or SO4 or heavier atoms Please see the troubleshooting section to find out how to calcu late a more realistic dose in this case 3 5 Initiating data collection The values given in the Strategy table see section B 4 7 can be used for subsequent data collection using the Export Run Definition Recollect Test Images and Collect Data set buttons in the Strategy page ig 17 Export to Blu lce Recollect Test Images Collect Dataset Figure 17 Options after strategy calculation http www pnas org cgi content abstract 103 13 491 http smb slac stanford edu public research staff_publications IUCr 20Faster 20data collection ht 31 e Export Run Definition This button does not initiate data collection automatically but fills out a Blu Ice run entry The user can then open a Blu Ice client and start the data collection This option is useful if the user wishes to modify certain beamline operation parameters which are not accessible from Web Ice e g dose mode or beam size or to queue the data collection run Some of the settings oscillation start and end oscillation angle exposure time detector and beamstop to sample distance and energy can be edited after clicking the button and before the run is exported e Recollect Test Images This is recommended if the user wishes to repeat autoin dexing and strategy calculation based on the warnings given by the s
39. n and autoindexing 3 2 3 Multicrystal strategy The multicrystal strategy mode allows to select the optimal starting and final orientation phi in cases where a full data set cannot be collected from a single crystal often because of radiation damage during data collection of microcrystals metalloproteins or samples at room temperature This option can be selected by choosing the multicrystal option in the Other Options setup page fig D Upon selecting the multicrystal strategy option the strategy calculation program will change to MOSFLM and a menu to select multicrystal strategy options fig 12 will ap pear Multicrystal Options Previous run in the multicrystal series guillermol Leave blank if this is the first run in the series Rotation angle in degrees to be collected from this crystal 10 0 Must be at least 1 degree or blank Crystal 1 Start angle 242 0 End angle 252 0 Figure 12 Options for multicrystal strategy If the crystal mounted is the first one in the multiple crystal experiment the Previous run in the multicrystal series input box must be left empty Once a strategy calculation run has been calculated for the crystal a file containing information about the orientation of 23 the crystal and the associated strategy is written out in the webice directory for the run When another crystal in the multicrystal series is mounted the immediately preceding run must be selected using the drop down me
40. n as starting point for image file browsing If it is set to No a specific Image Directory may then be given The Image Directory will be updated every time the user selects an image for display with the Image Viewer Show Overlay Spots If this option is set to Yes the Image Viewer will display the SPOTFINDER generated image highlighting the spot positions ice rings and resolution limit This option should only be set to Yes in conjunction with the next option Automatically Analyze Image Automatically Analyze Image When set to Yes the Image Viewer will automati cally run SPOTFINDER on the selected image If set to No the user must click the Analyze Image button in the Image Viewer tab to analyze a specific image 7 4 Autoindex Configuration Autoindex Configuration er Screening F alr Automatically Update Run Log yes Figure 32 Autoindex configuration options e Use Global Image Directory When this is set to yes the Autoindex Viewer will use the directory specified in the General Configuration see section Z 2 as starting point for image file browsing If it is set to no a specific Image Directory may then be given 46 7 5 Number of runs per page This sets the maximum number of runs which will be loaded and displayed on a single page in the All Runs frame It is recommended to keep this number below 20 as loading a large number of ru
41. nitor the experiment e Preferences The Preferences tab shows the user information and permissions and system and user set preferences for the session The user can select a beamline using the drop down menu on the top bar and clicking the Select button fig T When a beamline is selected the user can view the images as they collected as explained in the Image Viewer section see section2 LI Selecting a beamline is required to calculate a data collection strategy specific to the beamline in question as described in the the Autoindex Tab help see section B 2 and to access the beamline video feed Help Logout Beamline Select beamline x Figure 1 Detail of the Web Ice interface window showing the Beamline Selection tool and links to log out and the on line documentation Clicking the Log out button exits Web Ice The user will have to log in again in order to continue using Web Ice The connection to the web server will also be reset if Web Ice is left idle for 30 minutes To access the on line Web Ice documentation click on the Help link at the right of the Web Ice window This will open a new browser window with specific information on the tab the user is currently visiting 1 5 New features 1 5 1 2015 1 Strategy determination has been further streamlined for speed The selection of the program MOSFLM or BEST is done automatically 2 When the user provides the number of anomalous sites and number of resid
42. ns simultaneously may cause performance problems Reverse Autoindex Log When set to yes the Autoindex Log displays messages in inverse chronological order i e the latest message appears at the top of the log Reverse DCSS Log When set to yes the Beamline Log displays messages in inverse chronological order i e the latest message appears at the top of the log Automatically Update Run Log When set to yes the autoindex log in the Se lected Run Log page will be automatically updated as the autoindexing and strategy calculating programs run If not an update button will appear on the log Screening Configuration Result El Pon Ascending gt Figure 33 Screening configuration options Automatically Update Screening Output If set to yes the screening results will be refreshed automatically in the Cassette Summary see section 1 and a link to the results will be generated in the Cassette details see section 2 Update Rate sec How frequently the screening results are updated This only applies if the Automatically Update Screening Output option is set to yes Column Display Options This can be used to select the columns displayed in the Cassette Summary see section 5 1 Original Displays only the columns present in the user s spreadsheet Minimum Displays the cassette port number crystal ID protein name and the comment column Results Dis
43. nu This will automatically read in and use the file storing the strategy parameters for all previous crystals in the series and updated with the values determined from the current sample The user can specify the expected rotation range that can be collected from the crystal before damage takes place in the rotation angle input box which defaults to 10 degrees For the first sample accurate selection of the rotation range is not critical and could be even left blank in this case the program will calculate the standard range to maximize completeness for the crystal symmetry and orientation However in general a fuller completeness will be achieved with a more accurate estimate of the rotation range based either on the dose calculated by the strategy or the actual decay observed from previous samples When a previous run is selected the program displays the starting and end phi angle determined by the strategy for the previous runs If these values do not match the data collected from the crystal they can be edited to reflect that data that is actually available for example if the crystal was either damaged earlier or lasted longer than the input rotation range Note that for multicrystal MAD and SAD experiments the input angle range will be used unlike in single crystal mode where twice as much data are collected by default to improve the multiplicity 3 2 4 Importing the screening strategy If the sample has been mounted and analyzed
44. of how spots are chosen for autoindexing e Too few unimodal Bragg spots x in image e couldn t find 3 good basis vectors There errors usually indicate high mosaicity or low crystal overall quality Occasionally Autoindex may fail with a MOSFLM error See previous Question Q My crystal is pseudo cubic with the true symmetry being rhombo hedral I want to use Web Ice to calculate the phi rotation strategy so I tried entering the known Laue group and unit cell in to the Autoin dex run setup This failed Autoindexing also failed when I gave just the Laue group How can I get the right strategy In many cases entering the known symmetry and cell is a good way to handle pseudo symmetry However this is a very special case As shown by the LABELIT indexing log file your crystal can be indexed in four possible rhombohedral settings depending on which body diagonal of the primitive cell is taken as the threefold These four cases cannot be distinguished until the data are integrated and symmetry related intensities are compared Still if radiation damage is a problem there is a way to identify the threefold with minimal initial data Follow these steps 1 Collect 1 degree oscillation images at 0 1 2 3 degrees and 90 degrees 2 Use Web Ice Autoindex Tab to index on the 0 and 90 degree frames Now navigate to the Details button to display the name of the Unix directory that contains the processing results 3 Open a Unix c
45. olution and refinement Collaborative Computa tional Project Number 4 Acta Cryst D50 760 763 1994 e XTRIAGE data quality assessment P H Zwart R W Grosse Kunstleve and P D Adams CCP4 newsletter 43 2005 For additional information about the Web Ice project please see http smb slac stanford edu research developments webice 1 2 What is needed to run Web Ice You need an account on the SSRL Macromolecular Crystallography computers New accounts can be requested by fooling the instructions at http smb slac stanford edu facilities computing account htm Your data needs to be stored in the SSRL MC file system default when collecting data at the MC beamlines The system does not support image download from remote computers Some software in Web Ice uses information from the image header in order to reduce the need for user input this means that only SSRL collected images are actively supported by the software The browser must be set to accept cookies in order to log in to the Web Ice appli cation Javascript should be enabled in the browser in order to have access to all the Web Ice features 1 2 1 Supported browsers The Web Ice interface has been optimized for Firefox v 1 5 or newer and Internet Explorer v 6 or newer Since May 2007 the javascript applications work under Safari 1 3 How to start Web Ice 1 Launch a browser window from any computer and enter the URL gt z 2 Lo
46. ommand shell and change to that directory Issue the command labelit rsymop 1 4 this integrates the first 4 degrees of data and helps identify the correct setting 4 Again in Web Ice return to the Autoindex results and hit the Setup button Request the additional integration of the correct solution verify which solution number cor responds to the correct setting in the Autoindex solution list and hit Submit When this is complete proceed to the Strategy button select the correct solution number in the solution selection box and read off the optimal phi rotation range from there http adder lb1 gov labelit html manual htm 51 Q How can I verify that the data collection strategy is calculated cor rectly 1 Inspect the results saved to your disk area using the Details see section 3 4 6 link 2 If you do not agree with the input used to calculate the strategy e g mosaicity resolution limit or other assumptions made about the sample you can edit the input command files written out by Web Ice and re run the programs from the command line on the blcpu computers e To run BEST edit the file run_best csh in the subdirectory solution space group if BEST is used as the Strategy Program or in the BEST subdirec tory if MOSFLM is used as the Strategy Program then run it as source run_best csh Consult the BEST docume fatio e To run the MOSFLM strategy edit strategy mfm and or strategy_anom mfm
47. play information about the image and the autoindexing results e Header The Header tab displays the image header Table D e Analyze Image This tab displays the image analysis results see section 2 5 The analysis results logs and JPEG images are stored together with the user s data under the directory crystal analysis e Crystal Image The Crystal Image tab displays the crystal snapshot JPEG file e Autoindex This tab displays the autoindex results from LABELIT see section B 4 Autoindex will be carried out if two images at different crystal orientations are collected Image or images collected at a third orientation will not be used for the autoindex e Details The Details tab lists all the output files from autoindexing The results are stored together with the user s data in the directory listed at the top of the Details view The files named indexXX and indexXX_S mat are the MOSFLM input script and matrix used for solution number XX By clicking on a file name the contents will be displayed on a separate browser window The bottom frame contains the cassette browser tool It displays an array corresponding to the ports in the cassette or unipuck The ports that contain valid crystal id are displayed with links otherwise they are grayed out When the user clicks one of the ports the first image collected for that port will be displayed The Analyze and View Strategy buttons have the same functionality as in the Cassette
48. plays the same columns as the Minimum display plus the columns containing the screening results generated by the screening software All Displays the original spreadsheet and the results columns 47 e Image Display Options These options determine the information shown in the 7 6 Images column of the Cassette Summary see section 5 1 Hide images Displays only the image name Show Image links only Displays the results of the diffraction image analysis for the images collected at different crystal orientations during screening and links to the diffraction image and crystal snapshots Clicking on the links opens a window displaying a JPEG file Selected Sample only Displays the results of the image analysis and diffrac tion image and crystal snapshot JPEGs for the sample selected by the user e Crystal Sorting Column By default the samples will be sorted by the column selected in this option Crystal Sorting Direction By default the samples will be sorted in the order ascending or descending selected in this column For example if the Crystal Sorting Column is Score and the Crystal Sorting Direction is Descending the highest scoring samples will be displayed first Video Configuration Video Configuration Hutch Camera 5 alea ea Robot Camera Update Rate see Figure 34 Video configuration option
49. re autoindexing the optimal collection range is calculated for all the lowest symmetry group in the predicted lattice The full recommended data collection strategy for the determined space group is dis played at the bottom of the page The BEST strategy calculation results can also be dis played by selecting the appropriate tabs above the data collection strategy table fig oll Clicking on the phi ranges displayed in the table will toggle between the strategy to opti mize anomalous data and unique data completeness http smb slac stanford edu facilities software blu 1ce scan tab html output files Before September 2015 the software calculated the strategy for all the space groups this took a long time and has been discontinued 28 Space Group P222 _Strategy _ Figure 16 Strategy navigation tabs to toggle between the strategy summary table and the completeness and overlap analysis for each Laue class in the autoindexing solution The Data Collection Strategy table shows all the required input for a Blu Ice data col lection run based on the strategy calculation results Below is an explanation of how each quantity is determined If the results are not suitable for the users experiment it is pos sible to re run the calculations as explained in the troubleshooting section see section e Experiment type This will also display a warning if a non default total oscilla tion range is selected in the Space Group Table e g if th
50. ry andplots 2 02 0008 35 443 Detail ss hw i Saw sus BS BG we es 2G 36 4 5 Reprocessing the dat 00200008088 36 37 See a 38 511 Screening Resultg orinar YR OY RS 38 O gered etal pede E eden 40 ee ee ee ee ee 40 pedos eee ee Dri 40 sag eek at er as Siete Gate Goats 41 A es 41 1 pdating Sr 41 2 assette Detail Mae s Sew e A ek OVS gel Se Sr AO eee oe ee RO A eed 42 6 Beamline status 43 6 1 Beamline Selection 43 62 Beamline Videdl 43 ou ee ae a a 43 6 4 _Experimentlog 000000000000 00004 44 45 7 1 Saving the Preferences 45 72 General Configuration 0 00 0002 eae 45 7 3_ Image Viewer Configuration 02 0 2 00 0004 46 7 4 Autoindex Configuration 00 008 a 46 7 5 Screening Configuration o o e 47 7 6 Video Configuration o o a a e e a a 48 S_ Troubleshooting 49 1 Getting Started 1 1 A brief introduction to Web Ice Web Ice is a web browser application designed as a high level interface to PX experiments at synchrotron beamlines Web Ice can be used to access screening and autoindexing results 24 7 remotely or locally In addition Web Ice can be used during beamtime to monitor the beamline instrumenta tion and control panel via the beamline video system view diffraction images as they are collected and calcu
51. s Displayed Camera This option controls what video feed is displayed by default in the Video page Selecting All will display all video feeds If the user s bandwidth is limited it may be more advantageous to display one video feed at one time Camera Update Rate The user may choose how often in seconds the video refreshes the image for each camera Shorter times provide a more smooth live video at the expense of bandwidth usage 48 8 Troubleshooting Q I have typed the name of the image file in the File input box but the JPEG file is not displayed and the right frame displays Failed to load image header Make sure that the image exists ie no typos and is readable You must type the full path to the image input window alternatively try using the file browser in the bottom frame Q I get an HTTP error when trying to display or refresh a page HTTP errors may be caused by transient glitches communicating with the server Try again If the problem persists tell the user support staff Q In the Autoindex tab the Runs table does not get loaded properly the fields for the runs are empty when trying to display the run contents the browser displays an impersonation server error If this problem happens try reducing the number of runs displayed per page in the au toindex tab options in the Preferences tab If the problem persists there may be a large number of users trying to connect to the impersonation
52. s 3 3 1 Aborting autoindexing The user may choose to abort the data collection or autoindex run by clicking the Abort button displayed after starting autoindexing fig 13 FGSP Setup Logs Autoindex Summary Solution Predictions Strategy Details Update Figure 13 Running Autoindex 3 4 Viewing the run results The Selected Run displays a series of links fig T4 to facilitate viewing all the run anal ysis results 25 rnase H6 Setup Logs Autoindex Summary Solution Predictions Strategy Details Figure 14 Selected Run navigation links 3 4 1 Scan The Scan page only appears if the Perform Fluorescence Scan option was selected for a MAD SAD experiment This page will display a graph showing the raw fluorescence counts as the scan is being carried out as well as messages from the scan operation Once the scan is processed with autochooch a plot of f and f will also be available The plots can be saved as PNG images by right clicking on them and selecting the Save Image As option from the menu 3 4 2 Log The Log link allows the user to inspect the detailed autoindexing log with information about each program and version that is run and exit status and data collection status on the connected beamline The latter log is shared with 3 4 3 Autoindex Summary The Autoindex Summary page displays the refined values for the direct beam coordi nates Beam x and Beam y and the distances an
53. sible autoindex solution e The solutionxx subdirectory contains the integration results for the solution number xx since 2015 the results for the triclinic solution are not calculated It also contains the dose calculation results in the RADDOSE directory and the strategy input scripts and log files for each possible symmetry consistent with the autoindexing solution in directories named after the corresponding Laue group e The SCAN directory contains all the output files from the fluorescence scarf if a MAD or SAD experiment has been selected These files are also written to the image directory e If MOSFLM is chosen as the strategy program a BEST directory containing the input and log files from the program BEST used to calculate the exposure time will also be generated 3 4 7 Strategy The strategy calculation results are shown under the Strategy tab The optimal oscillation range for the Laue group determined by LABELIT and the overall completeness are displayed in the Space Group table fig 15 An upper limit for the os cillation per image delta phi is also shown in this table Above this delta phi value more than 3 reflection in one or more images in the phi range will overlap Note The maxi mum delta value is based on the mosaicity estimation If the mosaicity is underestimated the delta phi value will be overestimated Figure 15 Space group summary table Unless the space group was preselected befo
54. side of the display image These buttons only work if an image has already been loaded The Prev button loads an image with the immediately lower index than the current image For example 1f the current image is remo_3_015 img clicking the Prev button will load remo_3_014 img Similarly the Next button loads the image with the next higher index than the current image In the previous example clicking on the Next button instead will load remo_3_016 img If the current image is the first or last image in the dataset clicking the Prev or Next button respectively yields no effect 2 1 1 Displaying the last image collected If the user has selected a beamline where an experiment is being carried out the Last Image button will be active By clicking this button the user can display the latest image written to the directory by the beamline control software 11 2 1 2 Using the file browser for image selection The first line in the file browser displays the current directory Clicking on Refresh will reload the directory contents this is useful for example if new images are being continuously written to the directory Clicking on Up will change the directory to the parent of the current one The following lines are links to subdirectories or image files File permissions file directory name size in bytes last modification date and time are displayed for each file Clicking on a subdirectory name will list the contents of that subd
55. st screened sample Import Run Name FGSP Collect 2 images and autoindex for beamline BL1 5 Autoindex existing images Create Run Cancel Figure 6 New run form page Pressing the enter key or clicking the Create button will create the run clicking on the Cancel button will return to the user Runs page The Run generation tool requires javascript enabled on the browser 3 2 1 Autoindexing existing images This option assumes that the user has already used Blu Ice to collect the diffraction images and for anomalous dispersion experiments the fluorescence scans required to character ize the sample In this case Web Ice can read these files and supply a data collection strategy to the user The option is selected by clicking the Autoindex existing images button in the new run form page fig 6 and clicking the Create button This will take the user to the Setup page which guides the user through the following run set up steps The Prev and Next buttons can be used to navigate between the various steps 1 Choosing the images The directory and image names can be entered by the user or selected using the Browse button fig 7 2 Choosing the strategy The user has the option to select the strategy using beamline specific parameters this option is disabled unless the user has selected a beamline figl this option takes into consideration the detector position and energy limits enabled at the beamline and uses th
56. ter will be selected instead e Resolution This is the resolution for which the strategy has been calculated A warning is displayed if the maximum resolution predicted from the image integra tion statistics shown under the Autoindex and Solutions links is higher than the value at the detector edge 29 e Exposure time BEST is used to estimate the optimal exposure time to collect data with an I oJ of 2 at the resolution given above For SAD and MAD experiments the 1 01 target is chosen so that a default signal of 3 can in principle be measured at low resolution If the user provides the number of anomalous scatterers in the molecule the signal will be estimated from that amount Note While this is a better criterion to determine the strategy in phasing experiments theory and reality may differ If the expected anomalous signal is small increasing the data multiplicity beyond what is recommended by the software may be a good course of action If the exposure per image is too short it will be reset to the minimum allowed value in this case a suitable beam attenuation will be calculated to avoid image overexposure e Attenuation Calculated to avoid too short exposure timed e Detector to sample distance Detector to sample distance to obtain the resolution given above If the predicted resolution is shorter a warning will be displayed with the required sample to detector distance Note If the detector distance to achieve th
57. the Show spot overlay check box to toggle between displaying the high lighted spots ice rings and resolution limits or the original image The output image displays the following features 13 Header Name OVERLOAD_CUTOFF HEADER_BYTES DIM BYTE_ORDER TYPE SIZE1 SIZE2 PIXEL_SIZE BIN DETECTOR_SN TIME DISTANCE PHI OSC_START OSC_RANGE WAVELENGTH BEAM_CENTER_X BEAM_CENTER_Y PIXEL SIZE EXPOSURE TIME TWO THETA DETECTOR Table 1 Header fields for a Q4 image Description The maximum intensity value for each pixel Length of the header Image dimensions Machine byte order little or big endian Type of stored value for each pixel Width of the image in pixel Height of the image in pixel Size of the pixel in cm Detector binned mode Detector serial number Exposure time Detector to sample distance Phi Starting Phi Omega Oscillation range Wavelength in Angstrom Beam center X in mm Beam center Y in mm Size of the pixel in mm Exposure time in seconds Two theta angle of the detector not supported at SSRL Detector name 14 Example 65535 512 2 little_endian unsigned_short 2304 2304 0 0816 none 403 30 041451 175 000000 89 000000 89 000000 1 500000 0 979413 94 000000 94 000000 0 0816 30 0415 0 ADSC QUANTUM4 Good spots potential Bragg spots green border Dubious spots overloaded weak ice diffraction etc yellow border e Spot maximum pixel White dot more than
58. tion edge energy for SAD or MAD and the detector type installed at the beamline The default attenuation corresponds to the current value at the beamline usually no attenuation is necessary for the test images except for BL12 2 Changing the res olution will make the detector move at the start of the image collection The Laue symmetry and cell can also be given if known see sectionB 2 1 the multicrystal strategy mode see section B 2 3 can also be selected here this will change the strategy program used to calculate the oscillation range for data collection from BEST or MOSFLM For SAD and MAD experiments The number of heavy atoms and the number of residues per monomer may be also specified here If given they will be used in the dose calculation for the strategy 22 Choose Other Options Prev Next Please enter values for optional parameters or leave the entries blank Test Image Collection Options Exposure Time b Default 2 se Oscillation Per Image k Default 2 Attenuation 7 64 Default 30 53 Target Resolution 1 39 Default 1 39 A Energy 9021 52 eV Detector Distance 93 74 mm Autoindex Options Laue group Don t know gt Unit cell a bf qf af a A j Cell parameters are optional but if given a Laue group must also be specified Number of heavy atoms in monomer 10 Number of residues in monomer boo Optional if given it will be used in dose calculation Figure 11 Options for test data collectio
59. trategy Click ing the button allows the user to edit the oscillation angle exposure time detector and beamstop distance and energy before recollecting two images and repeating the analysis e Collect Data Set This button starts data collection The user may edit the os cillation start and end oscillation angle exposure time detector and beamstop to sample distance and energy before data collection is initiated Important Web Ice will recalculate the dose when the exposure time attenuation or oscillation range are changed in the Export Collect page However the resolution does not change The resolution corresponds to the diffraction limit of the crystal and it is difficult to predict the new resolution when the exposure is changed without analyzing another pair of test images first 4 Data processing The tab Process is used to process data sets and optionally to attempt structure solu tion by molecular replacement Data autoindexing and integration are carried out with LABELIT and XDS The data are analyzed with POINTLESS and XTRIAGE scaled and merged with SCALA and transformed to amplitudes with TRUNCATE If a PDB file is supplied MOLREP is run and the best solution is refined with REFMACS Selected statistics and graphical output from these programs is displayed on the results pages Input scripts and full log files are written to disk under the data SUSER webice process directory These files can also be inspected
60. ts further inspection or it can be safely discarded e Crystal JPEG Snapshot file name e Spot Shape Mean value of the longest spot dimension divided by the shortest one It is between 1 5 and 2 for good crystals e DISTIL Resolution Resolution estimate by the LABELIT SPOTFINDER mod ule based on the number of spots in resolution shells e Ice rings Number of ice rings e Diffraction Strength Average spot intensity 39 e Score The score for the individual image 0 or usually indicate no useful diffrac tion A sample scoring higher than 4 5 may merit inspection Very different scores for images at different orientation indicate anisotropic diffraction or a badly cen tered crystal this can be confirmed by inspection of the Crystal JPEG 5 1 2 Selecting samples A sample is selected by clicking the radio button in the port column fig 25 only one button can be selected at a time Port E Al Figure 25 Selecting the sample row Al 5 1 3 Data collection strategy A data collection strategy will be calculated during screening if the sample stays mounted on the goniometer head after the screening shots i e by inserting a Stop in the screen ing task sequence in Blu Ice see the Blu Ice User Manual In this case the View Strategy button will direct the user to the Autoindex Tab see section B 4 from which the strategy results can be viewed once the strategy calculation is complete If the strategy calcu
61. u can see the autoindexing results from LABELIT by following the Details link in the Autoindex Tab or in the Cassette Details page in the Screening Tab and clicking on the labelit out file For experienced MOSFLM users The Details page also contains the input and output MOSFLM files called index and index out with the number corresponding to dif ferent LABELIT solutions Often the error will happen when integrating the triclinic solution 1 e examine the index01 out file You might be able to integrate the images by tweaking the input parameters in the input files Q What do the System Errors displayed in the Spreadsheet mean In most cases a system error indicates that a autoindex solution could not be found a No_Indexing_Solution error message is given in this case followed by the specific cause e Too few non ice spots x in image e Too few candidate Bragg spots x in image e Too few good Bragg spots x in image These three errors simply indicate that there are not enough spots for reliable au toindexing Inspect the crystal JPEG image in the Screening Cassette Details page to verify that the crystal is hit by the beam the crystal should be roughly in the mid dle of the image Re mounting the crystal and centering manually and adjusting 50 the beam size to decrease the background may help Weakly diffracting crystals may need longer exposure See the LABELIT manual for a detailed explanation
62. ues the program uses the information to calculate the strategy for MAD and SAD experi ments 1 5 2 2014 1 When the crystal point group Laue group is provided by the user via drop down menu the data collection strategy is only calculated for that particular symmetry This cuts down the calculation time considerably 1 5 3 2013 1 Multicrystal strategy calculation option in the autoindex tab Useful for microcrys tals room temperature data collection and samples particularly sensitive to radiation damage 1 5 4 2012 1 Faster preparation for data processing 2 If the space group is provided as input to strategy calculation the strategy will only be computed for P1 and the given space group This can save some time for high symmetry groups 1 5 5 2011 1 Implementation of a data processing and structure solution tool based on an Autodrug workflow 2 New button to recalculate the dose when a different number of images or crystal exposure is selected before exporting the strategy to Blu Ice 1 5 6 2010 1 Supporting strategy calculation for the PILATUS 6M detector thin phi slices are used with this detector 1 5 7 2009 1 Increased data multiplicity for MAD and SAD experiments 2 Using the latest version of RADDOSE 2008 This version gives a better estimate of the absorbed dose for higher energies 3 An optimal exposure time is calculated for each space group 1 5 8 2008 1 Generation of an exec
63. uring processing or find bugs SecondMutant Setup Logs Summary Plots Details Update Output Log Error Log _Update Log 16 09 27 Setting up environment A 16 09 32 Extracting names from data ana JASON M116A m116a a8_ 8 0001 img 16 09 51 Parsing image header info 16 09 51 Extracting names from data ana JASON M116A m116a a8 8 0001 img 16 09 51 Extracting names from data ana JASON M116A m116a a8 8 0720 img 16 09 51 Reading image header 16 09 51 Checking oscillation angles between image number 1 and 720 16 10 23 No jump in oscillation angles 16 10 23 Running XDS XYCORR INIT COLSPOT IDXREF 16 10 56 Error in XDS SOLUTION IS INACCURATE continue integration 16 10 57 Running XDS DEFPIX INTEGRATE CORRECT 16 14 22 Parsing XDS output file Space group from XDS C222 Unit cell from XDS a 32 68 b 86 30 c 65 98 alpha 90 000 beta 90 000 gamma 90 000 Figure 21 Data processing log 4 4 2 Summary and plots This page lists summarized results tables and plots extracted from the log of each pro gram 393 SecondMutant Setup Logs Summary Plots Details Update Refinement R Factor L Test Z Test L test 0 0 0 1 0 2 0 3 0 4 0 5 0 6 0 7 0 8 0 9 10 Acentric Observed Acentric Untwinned Acentric Perfectly Twinned Figure 22 Example of plot extracted from the program log files 4 4 3 Details The Details link can be used to browse the command files
64. utable shell script to re run RADDOSE manually 2 The screening results are updated automatically by default If the user prefers not to have automated updates they can turn off this feature in the Preferences tab The update button still works in either case 3 BEST can used instead of MOSFLM to calculate the oscillation range total and per image The MOSFLM strategy TESTGEN option is always used to carry out the spot overlap analysis over the entire range of rotation 4 The beam may be attenuated for collection of the test images used to calculate the data collection strategy The attenuation defaults to the value currently set at the beamline 5 1 5 9 2007 1 Extensive revamping of the Web Ice interface to facilitate navigation 2 Reorganization of files in the webice autoindexing directory to make it easier for users to locate the Web Ice input command files and logs used for strategy calcula tion 3 Improved image mark up in the Image Viewer and Screening Cassette Details pages The same diffraction image application is also used to display the Autoindex Pre dictions replacing the old Java tool 4 javascript applications have been modified to run under Safari 5 An improved BEST version 3 1 is used to calculate the exposure time 6 Several bugs in the strategy calculation have been fixed 7 Possibility to select any element from P to U for non optimized SAD experiments 8 Itis no longer required to select an exp
65. via the web ice application See the introduction to Web Ice see section T 1 T for the appropriate software references 32 4 1 Process Runs When the Process tab is selected the user is shown the Process Runs page which will be empty the first time Once a data set has been processed this page will list the user supplied dataset name creation time the name of the first image in the set and other information about the job status the Delete link can be used to clear the results from the data user webice directory and delete the dataset name the images will not be deleted Welcome ImageViewer Autoindex Screening Process Beamline Video ana Datasets New Dataset Selected Dataset Beamline Select beamline Sort By Dataset Name Ascending O Descending Update Dataset 1 9 of 9 first prev next Last Dataset Name Creation Time Ist Image Status Pid Host Commands D38GP39GV40G 11 04 05 14 06 38 d38gp39gv40g b6_7_0001 img not running 26968 adproc02 slac stanford edu Delete F54G B3 11 07 22 11 39 21 B3_F54G_1_0001 img not running 15650 adprocO1 slac stanford edu Delete P422 C2 11 07 07 17 48 30 B2 AK97_7_0001 mccd not running 15705 adprocO1 slac stanford edu Delete Y 14AY55E A F6 11 05 11 19 57 22 y19a f6_6_0001 img not running 29200 adproc01 slac stanford edu Delete YI4AYSSFD99A F6 ALL 11 05 12 15 04 24 y19a f6_6_0001 img not running 137
66. white dot in a spot indicates multiple maxima Initial estimate of the resolution limit Green circle e Ice rings Orange circles The results displayed by Web Ice include e Number of good Bragg candidates e Average spot model eccentricity The closer to 0 the more circular the spots are Very high values around 0 8 or higher may indicate high mosaicity e Number of ice rings e Resolution estimate e Maximum cell edge estimated from the distance between candidate Bragg spots e Saturation percentage of the overloaded value for the strongest peaks If it exceeds 50 there may be too many overloaded spots e Number of spots with overloaded pixels e A score for the image calculated as follows 1 A score is assigned depending on the resolution ranging from 14 for resolu tion higher than 1 5 A to 1 for lower than 8 A 2 The score is then adjusted by 5 to 4 points depending on the diffraction strength spot shape and number of ice rings 3 finally the score is normalized reset so that the minimum score is O for no diffraction Both the log and the overlaid image file generate by SPOTFINDER are saved in the di rectory data userid webice image For example if joeuser analyzes inf_1_001 img output files inf_1_001 1log and inf_1_001 spt img will be saved in the data joeuser webice image directory 15 3 Autoindex and strategy calculation The Autoindex Tab is used to autoindex test diffraction images
67. with the option to collect the test images too and to calculate data collection strategies that optimize data com pleteness It can also be used to inspect a data collection strategy generated during sample screening The autoindex and strategy results for each sample are grouped under as a Run Each run has got a unique name The autoindex Tab navigation toolbar see section 4 contains links to display a summary of all the user s runs under user Runs start an interactive application to generate new runs New Run or inspect or edit one of the runs Selected Run Figure 4 Navigation toolbar in the Autoindex tab 3 1 The Runs page The Runs page fig 5 displays a table summarizing all the autoindexing results generated by Web Ice Delete B2 BL7 1 Feb2007 pina ditty DS 87 18 i P3 Delete Delete Lo d 0 B LM n B3 BL7 1 Feb2007 86 y y P Delete AROS A T F A r B J i we Delete Figure 5 Autoindex tab page showing a summary of all autoindex runs For each run the following are listed 16 1 The images used for autoindexing 2 The crystal score calculated as 1 0 0 7 x e 4 1 5 x rmsr 0 2 x u where d is the resolution limit in A rmsr described above is in mm and is the mosaicity in degrees 3 The number of spots in the image and the number of reliable diffraction spots found after rejecting the weakest and strongest spots 4 The number of ice rings 5 T
68. x1s 2006 11 16 09 39 30 Summary Details Download Results Delete 5345 SMB_Oct_2006 x1s 2007 01 10 13 51 38 Summary Details Download Results Delete Upload new spreadsheet Figure 23 Spreadsheet list with links to the screening results Excel spreadsheet file and the Screening Database interface 37 Once a cassette has been selected it is possible to revisit the results for that cassette by clicking on the Cassette Summary and Cassette Details links in the Screening Tab navigation toolbar 5 1 Cassette Summary In the Cassette Summary view the spreadsheet is displayed in a table format fig 24 All rows each corresponding to a sample are displayed The columns and the contents displayed can be controlled by the display options set in the Preferences Tab see section 7 3 User Cassettes BL1 5 Cassettes Cassette Summary Cassette Details Spreadsheet ID 5345 Update Edit Crystal Analyze Crystal Al View Strategy Port CrystalID Protein Images IceRings Comment Score UnitCell Mosaicity Rmsd BravaisLattice Resolution 90 25 90 25 E i in 9 A ag AS myo eae e ee a 0 669 45 35 90 00 0 75 hos P3 P312 P321 P6 P622 1 38 A eee iS 90 00 120 00 90 34 90 34 e A7_003 lobin 9 5 057 ae MF myo ie EA eee a 0 739 45 33 90 00 0 70 las P3 P312 P321 P6 P622 1 34 A oes A AOS 90 00 120 00 Collected several data sets on 7 1 90 15 90 15 c A2_003 img 0 y eR myo 903 img probably trashed 0 825 45 14 90 00 0 08 O86

Web-Ice Manual - Macromolecular Crystallography

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