Evolutionary Trace Viewer 2.0 Manual April 5, 2007 Introduction The
Contents
1. BAA25305 1 0 126147 18 0 011468 s NP_031469 1 0 036697 NP_037033 1 0 036697 28 0 013761 Q62577 1 0 050459 27 0 016820 AAB50851 1 0 067278 26 0 010703 P04365 1 0 077982 23 0 059633 16 0 137615 BAA13453 1 0 275229 12 0 145538 JC2556 1 0 302752 P36992 1 0 302752 11 0 118015 6 0 135222 CAC82582 1 0 024793 CAC82583 1 0 024793 29 0 433368 AADO1586 1 0 008065 054819 1 0 008065 31 0 125000 NP_058896 1 0 133065 17 0 111022 AAD01700 1 0 072581 Q28864 2 0 072581 25 0 112903 P1976 1 2 0 008065 5812143 2 0 008065 30 0 177419 15 0 048387 S53325 1 0 233871 14 0 010215 13 0 214075 5 0 097828 4 0 032029 NP_006519 2 0 380531 NP_033390 1 0 380531 7 0 207487 3 0 016573 NP_006519 1 0 327434 NP_033390 2 0 327434 9 0 277158 2 0 072805 AAG00547 1 0 074766 NP_065131 1 0 074766 24 0 046729 AAK31336 2 0 121495 20 0 196262 Q9DAO1 1 0 317757 10 0 025701 AAK3 1337 1 0 343458 8 0 333939 1 0 322603 1 4 3 Pre existing NHX trees or BLAST results Some users may already have a tree or BLAST results which they want to run ET on The ET Wizard can take these files as input but keep in mind you must supply a PDB formatted structure file or corresponding PDB code Also the residues in the PDB file must match the reference sequence in the BLAST results file or tree file 1 4 4 No structure solution Very often researchers are interested in a protein which has not had a structure determined yet In this scenario searchi2. Download POE file PDB code 1 60 Next gt Cancel lt Prev Next gt Cancel Evolutionary Trace Wizard Evolutionary Trace Wizard DEK Provide download path When the Evolutionary Trace is complete the results The user has the option of providing a multiple will be downloaded to your specified directory sequence alignment in MSF format for Evolutionary Please provide the path to the directory that you Trace Select Yes and provide the file path to do this wantthe results to be downloaded to otherwise select No Ifyou provide your own sequence aligi Oves Download path flocalpath lt Prev Next gt Cancel lt Prev Next gt Cancel Evolutionary Trace Wizard Evolutionary Trace Wizard DER Run Evolutionary Trace Identical sequences will be removed a Fragments will be removed Use the advanced button to access expert parameters Tree generation method UPGMA using matrix blosum62 for input to the Evolutionary Trace Structure Trace results are mapped onto query_1LBD pdb derivec Clicking finish submits your information to the Name of sequence to map onto structure query_1LBD EVOM Onay Trace server When your trace ls An ET Viewer project file will be created in 1LBD etvx completed the results will be downloaded to your Paatela Traca Opiania anecied computer Clicking Cancel will abort this process Downloading PDB file and you will be unable to view your trace results command downloadpdb2 p 1LBD output Saved
3. code needs to be supplied to the ET Wizard Figure 1 The ET Wizard can be used to submit information for running traces A On the first page the user is required to provide either the path to a PDB file or the code to be downloaded see example In either case a 4 character code should be provided Supplied structures should contain a single chain to be traced B On this page the user can supply a custom set of sequences These sequences MUST be in unaligned FASTA format and must be included in a single file see example Figure 3 If the user already has an aligned set of sequences item B should be left as No and the alignment provided on the next page C In both cases whether the set of sequences is aligned or not the user must provide the name of the sequence that corresponds with the structure file provided on page A This sequence must be identical to the structure file or the Evolutionary Trace will not work Also ensure that the header for each sequence in the input file follows the BLAST format that is the greater than symbol gt followed by the sequence name or identifier followed by a space D ET Wizard needs to know the local path to which the user would like the ET results downloaded to E Pressing the advanced button gives the user access to many features not fully supported at this time Most notable however is the Real Value trace option Default is to run a Real Value trace but users can switch to integer value tr
4. family ET can be performed from a variety of starting points Typically a new trace is run by providing ET with a structure file in PDB format that is representative of the protein of interest A trace can also be initiated with an existing multiple sequence alignment GCG format phylogenetic tree NHX format list of sequence names from BLAST or a list of sequences in FASTA format In all of these cases it is most useful to provide a PDB structure since the power of ET is visualization of ET residues on a 3 dimensional structure In fact when running ET via the ET Wizard you are required to provide a structure and or PDB code to successfully complete ET ETV was implemented in Java and consists of four major modules The Structure Viewer Tree Viewer MSF Viewer and ET Wizard These four modules are closely integrated so that ET results can be quickly viewed and edited or modified and rerun Output in the Structure Viewer is synchronized with the Tree Viewer and the MSF Viewer Interactive selection of sequences in the Tree Viewer can be simultaneously shown in the MSF Viewer and vice versa Selection of a set of sub family sequences can be used to run modified traces as may be required for sub family analysis ETV is launched via Java Web Start technology which uploads the initial application to the client machine and automatically checks for updates during subsequent start ups when a network connection is available Although the ET Viewer i
5. it in the selection dialog 1 1 6 Viewing modes ETV has a few basic viewing modes to aid in evaluation of trace results 1 1 6 1 Gobstopper color This coloring scheme is best visualized with the rank slider all the way to the right Prismatic coloring allows the user to identify the relative ranks of every residue in the protein by their color The order is red orange yellow green blue magenta with red amino acids being the most important residues and magenta residues being the least important 1 1 6 2 Color by cluster When the protein is visualized with this coloring scheme trace residues are colored according to how large the clusters are at a particular rank The clusters are colored in order of descending size as follows red blue orchid green purple cyan turquoise brown coral magenta orange sky blue violet gold When a residue is not of a cluster it is shown as black 1 1 6 3 Background The background dialog allows the user to customize the background color of the viewer 1 1 6 4 Backbone To view trace residues that reside in the interior of the protein users can select backbone viewing mode This mode shows only the backbone atoms of each residue 1 1 6 5 Viewing modes The user has a choice of two viewing modes space fill or bonds Space fill simply draws a sphere of Van der Waals radius for each atom while bonds mode draws a line between each atom Residues that are ranked at the current rank slide
6. pdb1LBD ent Extracting chain sequence from PDB fie command ExtractSeqFromPDB3 pl pdb1LBD ent query_1L output Advanced BLAST search command blastall p blastp d nr I T i query_1LBD fasta lt Prev Finish Cancel 1 4 2 Optional input Some users want to run ET on existing protein alignments or sequences The ET Wizard accommodates these users by allowing input of preexisting alignments or sequences Users still need to supply a protein structure to map results onto The alignment needs to be in GCG format in order to work If a list of sequences is being submitted they should all be in one file and conform to FASTA formatting Some users already have an alignment but it isn t in GCG format There are two ways to handle this The first is to open the alignment in another alignment viewer and save the alignment as a GCG formatted file This will preserve the alignment and allow it to be input directly into the ET Wizard The second method is to open the alignment in our MSF Viewer and save the sequences as a input file all sequences should be selected first This can also be used as input for the ET Wizard however the sequences will be realigned by ClustalW Any time sequences are saved in the MSF Viewer all gaps are removed in preparation for realignment Figure 2 Sample ETV file SamplePDB pdb REMARK access Revision 3 1 Date 1995 05 22 20 18 50 REMARK Args v i bik pdb o pt_lbik pdb REMARK algorit
7. AVA RSSDGSRITVROPOLMCLGPNFTLHRNSAQOQAGVDT LGIKMKRLDVTRAELGVL F RGLKCQKEIDGMR HCKQOQHPSEDGRFAQLLLRLPALRSISLKCLDHLNFI LDSFIVEMLDMP LEAELAVEPKTESYGDMNVENSTNDPVTINICHAAD TLVEWAKRI PHFSDLTLEDQVILLRAGWNELLIASFSHRSVSVQD HRSSAHSAGVGS I FDRVLTELVSKMKDMOMDKSELGC VLFNPDAKGLSNPSEVETLREKVYATLEAY TKOKY PEQPGRFA GLKCLEHLFFFKLIGDTPIDSFLMEMLETPLOI G gt G G L gt S W E gt S G LEAEMRVEQPAPSVLAQTAASGRDPVNSMCQAAPPLHELVQOWARRIPHFEELPIEDRTALLKAGWNELLIAAFSHRSVAVRDGI HSAHGAGVGDI FDRVLAELVAKMRDMKMDKTELGCLRAVVLFNPDAKGLRNATRVEALREKVYAALEEHCRRHHPDQPGRFGKLL LKCLEHLFFFKLIGDTPIDSFLLNMLEAPAD LLETESLVADPPEEFOFLRVGPESGVPAKYRAPVSSLCOIGNKOIAALVVWARDI PHFGOQLELEDOQILLIKNSWNELLLFAIAWR ENVDSRSTAPPOLMCLMPGMTLHRNSALQAGVGOI FDRVLSELSLKMRTLRMDQAEYVALKAI ILLNPDVKGLKNKPEVVVLREKM FSCLDEYVRRSRCAEEGRFAALLLRLPALRSISLKCFEHLYFFHLVADTSIASYIHDALRNHAPS References l Lichtarge O H R Bourne and F E Cohen An evolutionary trace method defines binding surfaces common to protein families J Mol Biol 1996 257 2 p 342 58 2 Mihalek I I Res and O Lichtarge A family of evolution entropy hybrid methods for ranking protein residues by importance J Mol Biol 2004 336 5 p 1265 82 3 Yao H et al An
8. Evolutionary Trace Viewer 2 0 Manual April 5 2007 Introduction The Evolutionary Trace Viewer ETV was developed to allow users a quick and easy method to view and run Evolutionary Traces Prior to development of the ETV users were required to use separate applications to analyze ET results The ET Viewer integrates visualization of all the available ET output and input into a single application to quickly evaluate Evolutionary Trace results Furthermore the ET Viewer provides the ability to initiate new traces and modify existing traces via the ET Wizard The Evolutionary Trace method was developed by Olivier Lichtarge to determine evolutionarily conserved residues within a protein family 1 The method was further developed resulting in the real valued ET 2 ET residues cluster significantly to elucidate functional portions of a protein 3 4 Identifying these important residues offers distinct advantages to protein researchers by narrowing their focus to specific regions of their protein ET clusters provide specific targets for mutational analysis competitive inhibition with peptides and other experimental techniques ET can also be utilized to identify sub family specific residues by use of the Differential Trace Analysis 5 This technique compares the ET results of a large super family trace with a smaller sub family trace consisting of sequences present in the super family and determines which residues are more conserved within the sub
9. T Red H K R Blue F W Y Green I L M V No color A C D E F P ET Wizard The ET Wizard is used to gather required information for running traces on our server Required and optional information is gathered from the user and submitted for processing via our ET Server Status messages are displayed in the ET Wizard as the trace is being run and the resulting trace files are zipped and downloaded back to the user s computer when the trace is complete The ET Wizard is responsible for the download and should stay open until the trace is complete in order to retrieve the trace results 1 4 1 Minimum input The minimum input for running ET is a PDB formatted file or valid PDB code Figure 1A The ET Wizard can check a supplied PDB code for validity and supply any existing chain information via the Protein Data Bank at http www rcsb org pdb The Evolutionary Trace can only run on single chains in the structure file thus the supplied PDB code needs to contain a chain specifier If no chain is specified ET defaults to the first chain in the PDB file or chain A When supplying a custom structure if more than one chain exists in the file then ET will always trace the first chain Example 1AO1 is the PDB code for a deoxyhemoglobin A which has 4 chains A B C and D In order to run a trace on chain B of this structure the user should input 1AO1B or laolb In all cases whether the user supplies the PDB file or not the PDB
10. accurate sensitive and scalable method to identify functional sites in protein structures J Mol Biol 2003 326 1 p 255 61 4 Madabushi S et al Structural clusters of evolutionary trace residues are statistically significant and common in proteins J Mol Biol 2002 316 1 p 139 54 5 Madabushi S et al Evolutionary trace of G protein coupled receptors reveals clusters of residues that determine global and class specific functions J Biol Chem 2004 279 9 p 8126 32 Mihalek I et al Combining inference from evolution and geometric probability in protein structure evaluation J Mol Biol 2003 331 1 p 263 79 Zmasek C M and S R Eddy ATV display and manipulation of annotated phylogenetic trees Bioinformatics 2001 17 4 p 383 4 Johnson J M et al Protein family annotation in a multiple alignment viewer Bioinformatics 2003 19 4 p 544 5 Thompson J D D G Higgins and T J Gibson CLUSTAL W improving the sensitivity of progressive multiple sequence alignment through sequence weighting position specific gap penalties and weight matrix choice Nucleic Acids Res 1994 22 22 p 4673 80 10 Thompson J D et al The CLUSTAL_X windows interface flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 1997 25 24 p 4876 82 IO PE EN
11. ace rank Typically maximum z scores are obtained at around 15 30 coverage which corresponds to the best clustering statistics We have found that z scores gt 3 0 that change smoothly with no large spikes are indicative of a good quality trace 6 ET Viewer files etv or etvx are simply a concatenation of ET files Users can modify this file if needed if they adhere to the following rules Figure 2 ETV files begin with the PDB structure file ET can only be run on single chains of a PDB structure and therefore the ETV file contains only a single chain Some users will want to visualize their trace results with other portions of the PDB file present such as ligands or other subunits in multimers This is accomplished by replacing the single chain PDB with the full length original or any portion of the full length original Keep in mind however that the PDB has no formatting rules prohibiting duplicate residue numbers in different protein chains This can cause problems with the ET Viewer since it attempts to match residue numbers from the ranks file with residue numbers in the structure file Another thing to consider is the total number of atoms present in the structure If there are too many ETV will suffer in performance depending on the user s computer After the structure information comes the ranks file information This contains the rank data from ET for each residue in the structure It is not recommended you change this as it
12. ace by un checking the Real Value option Pressing Finish takes the user to the status page F which displays the progress of the ET The user should not close the ET Wizard until the trace is complete since it is responsible for downloading the results of the Evolutionary Trace The results are downloaded as a zip file Included in the zip file are all of the generated data files from the Evolutionary Trace and the etv etvx file which is formatted so that the ET Viewer can read it Also included is a log file which details the output from the Evolutionary Trace server This file is important for keeping track of the settings used to run your trace as well as providing a means to troubleshoot the trace should it fail to run correctly A B Evolutionary Trace Wizard A Evolutionary Trace Wizard Structure File Custom sequence list Evolutionary Trace maps its results onto a structure Users may run an Evolutionary Trace analysis on The user can provide their own structure in PDB format or on a set of custom sequences These sequences must the ET Wizard can go and get it with a given PDB code be in FASTA format and included in a single file Make di e 1DIK ET can only run on single chains in PDB files sure to give the sequence name that corresponds to the Ensure that your custom file has only one chain or ifthe sequence in the structure file file is to be downloaded include a chain identifier 1 dikA O User supplied PDB file
13. e selection Individual sequences or sub branches can be selected by left mouse clicking the nodes as indicated by small boxes at each branch point Selected sequences are displayed as red text Selections are linked to the MSF Viewer section 1 3 when the associated multiple sequence alignment is loaded 1 2 2 Zooming Many traces have trees that are quite large Viewing the entire tree causes the sequence names to become unreadable You can make the tree larger by pressing the key Zooming back out is accomplished by using the key 1 2 3 Printing Printing in the Tree Viewer has not been enabled Printing can be accomplished by screen captures As some trees can be quite large it might be necessary to zoom in key and perform several captures of different parts of the tree After printing out the panels in an image editing program they can be taped together to form a banner 1 3 MSF Viewer The MSF Viewer provides a means to view multiple sequence alignments This module is unique in that it can be used independently of ETV files so that new traces can be run from existing alignments The alignment loader is from PFAAT v1 2 Bx 8 and is used to load GCG or FASTA ii E oe formatted alignment files When an N alignment is opened with its corresponding ETV file rank bars above each column in the alignment provide indication of each residue s relative rank The sequence that matches the structure will be highlighted
14. ersion information about ETV 1 1 3 Image export ETV has a rather rudimentary image export capability File menu It produces a fair reproduction of the current view in ETV Two file formats are available jpeg and png The image export does not work correctly on Macintosh computers in this release of ETV the color mappings are wrong Printing Printing and Print preview are also rather rudimentary at this time We recommend adjusting the view in ETV and doing a screen capture then printing with your 1 1 4 favorite photo editing software Alternatively the user can output scripts for PyMol or MolMol and print via those applications 1 1 5 Residue selection Residue selection can be accomplished two ways The first is via the residue selection dialog found under the Edit menu The selection dialog allows the user to select specific amino acids by residue number The other method is by mouse selection Either method will highlight the selected amino acid and give ET details of that amino acid in the status window Currently the mouse picker works best when the protein is shown in full space fill mode Clicking the protein in File in use 1LBD etvx z score 2 187 Rho 37 07 Percent coverage 100 0 backbone or bonds mode will still select atoms that are not visible causing misleading information to be output in the status window To deselect a residue merely click the amino acid again or uncheck the box next to
15. hm Richards qsort inline arclap REMARK radii Richards static VAW ATOM 1N SER 25 14 378 34 269 4 694 3 10 38 03 ATOM 2 CA SER 25 3 819 32 972 4 199 3 40 0 00 ATOM 3C SER 25 12 960 33 147 2 964 3 10 0 00 ATOM 40 SER 25 11 822 32 695 2 943 2 80 0 00 ATOM 5 CB SER 25 4 932 31 984 3 896 3 40 13 03 ATOM 6 OG SER 25 5 614 31 662 5 087 3 00 30 47 ATOM 7N CYS 26 13 515 33 813 1 953 3 10 0 19 ATOM 8 CA CYS 26 2 824 34 074 0 690 3 40 0 00 ATOM 9C CYS 26 11 461 34 703 0 924 3 10 0 09 ATOM 100 CYS 26 0 553 34 571 0 101 2 80 1 89 ATOM 11 CB CYS 26 3 666 35 005 0 177 3 40 19 50 ATOM 12 SG CYS 26 5 289 34 323 0 637 3 25 13 41 ATOM 13N GLN 27 1 339 35 400 2 048 3 10 0 32 ATOM 14 CA GLN 27 10 100 36 068 2 420 3 40 11 81 ATOM 15 C GLN 27 9 100 35 118 3 081 3 10 0 07 ATOM 160 GLN 27 7 896 35 361 3 058 2 80 26 12 ATOM 17 CB GLN 27 0 406 37 244 3 331 3 40 65 06 END ET_ranks Note in this file is a comment sign RESIDUE RANKS alignment residue type rank variability 2 HPA SAFVIG CL QRNKALT LKE EGKH RKIVQ N KQNRV FY YEVPSQ STYDE EQKRL KRAEDS EQDATNI 27 28 KREQHML 29 7 ELKNRGV 30 YVITAFL 31 C 32 GKEAVQ 33 iV 2 12 3 ee bie 25 4 a Oe BS TW vee te B 74 19 20 21 22 23 24 25 26 ETE E e E aTaanounan Na uksi Naw tree P00978 1 0 082569 P13371 1 0 082569 22 0 032110 pt_1bik 0 114679 21 0 007645 CAA36306 1 0 122324 19 0 003823
16. if it is available 1 3 1 Coloring schemes The MSF Viewer has three coloring schemes available Default see Table 3 ClustalX 9 10 and black and white Depending on your circumstances these schemes can aid you in evaluating your alignment Evolutionary Trace Tree jo PHFSELPLODOVILLRAGUNELL TAS 1 4 1 3 2 Sequence selection and saving Sequences can be selected by clicking on sequence names individually Selected sequences are shown in red If the current multiple sequence file is linked with the current ETV file then selected sequences in the MSF Viewer will also be selected in the Tree Viewer You can save the selected sequences from the MSF Viewer File menu item for input to run new traces If you just need to remove a few sequences choose Select All from the MSF Viewer Edit menu and then deselect the sequence names you want to remove Alternatively you may want to run traces on sub branches of an existing trace Sub branches chosen in the Tree Viewer section 1 21 will be selected to be saved in the MSF Viewer Selected sequences are saved in FASTA format as a input file This file can subsequently be used as input for running a new trace using the ET Wizard section 1 4 When used as input to the ET Wizard these sequences will be realigned using ClustalW Table 3 Orange G P S
17. lick will illicit descriptive text to be output into the status text box Right mouse button hold down Used for translating the protein along x and y axis Table 2 File Open ETV Results Pops up an Open File dialog in the user s home directory A file filter is defaulted to lt filename etv gt or lt filename etvx gt Open Alignment File Open a GCG or FASTA formatted multiple sequence alignment An alignment can be opened and viewed independently of ET results If an MSF file is opened while trace results are being viewed ETV will check to see if they are from the same trace and attempt to synchronize the structure viewer with the MSF viewer Close ETV File Removes the current file from memory and resets ETV to its default configuration Image Export Currently supports exporting to jpeg and png formats Currently this utility doesn t work very well It is recommended that users use a screen capture or utilize the PyMol or MolMol scripts to generate pictures Print and Print Preview Provides a method to print out to a printer although this doesn t work so well either It is recommended to capture the current view then use photo editing software to print or edit the image as an image export Future versions of ETV should contain better output control Exit Shuts ETV down Edit Search Inactive Will be used in future releases Residue Selection Lists every residue in the curren
18. ng the protein s sequence against the PDB using BLAST will return the closest homologs which can be submitted as a representative structure The ET Wizard requires a structure in order to submit a trace Figure 3 Sample input file gt AAC15588 GAPPEMPLERI LEAELRVESOTGTLSESAQOODPVSS ICQAADROLHOLVQWAKHI PHFEELPLEDRMVLLKAGWNELLIAAFSHRSVDVRDGIV LATGLVVQRHSAHGAGVGAI FDRVLTELVAKMREMKMDRTELGCLLAVVLFNPEAKGLRTCPSGGPEGESVSALEEHCROOY PDOPGRFAKLLLR LPALRSIGLKCLEHLFFFKLIGDTPIDNFLLSMLEAPSD gt AAC03056 RDITVERLMEADOQMSEARCGDKS IQYLRVAASNTMI PPEYRAPVSAICAMVNKOVFOQHMDFCRRLPHFTKLPLNDOMYLLKOSLNELLILNI QYVEPDRRNADGSLERROITSQQMCLSRNYTLGRNMAVOAGVVOIFDRILSELSVKMKRLDLDATELCLLKSIVVFNPDVRTLDDRKSIDL YASLDEYCROKHPNEDGRFAQLLLRLPALRSISLKCLDHLFYFQLIDDKNVENSVIEEFHKL 571292 NEEMPVE LDAELAVEPKTEAYMESSMSNSTNDPVTNICQAADKOLFTLVEWAKRI PHFSDLPLDDQVILLRAGWNELLIASFSHRSVTVKD LATGLHVH SAGVGSIFDRVLTELVSKMRDMOMDKTELGCLRAIVLFNPDAKGLSNPSEVEALREKVYAS LEGY TKHNY PDOQPGRFA LPALRS LEHLFFFKLIGDTPIDTFLMEMLEAPHOI 40081 EMPVDR SDOGVEGPGATGGGGSS PNDPVTNICQAADKQO LVEWAKRIPHFSSLPLDDOQVILLRAGWNELLIASFSHRS DGILLA HSAGVGAI FDRVLTELVSKMRDMRMDKTELGCL MFNPDAKGLSNPGEVETLREKVYASLETYCKOKY PEQOQ LLLR LEHLFFFKLIGDTPIDTFLMEMLEAPHO 701 1 DMPVER TEAYSDVNTESSTNDPVTNICHAADKO HF SDLTLEDQV RAGWNELLIASFSHRSVSVQD LATGLHV SAGVGS IFDRVLTELVSKMKDMOMDKSELGCL LSSPSEVESLRE LEAYTKOKY PEQPGRFA RLPALRS LEHLFFFKLIGDTPIDTFLMEMLETPLOV AAG24886 RDVTIERIHEAEREOLSEQKSGDNAIPYLRVGSNSMIPPEYKGAVSH OQTYQLIDFARRVPHFIN RCGWNEMLIA
19. of every alignment position of the current trace along with the structure s residue numbers If the user wishes to save the output a single menu item is associated with the Report Viewer that allows the file to be saved Alternatively the user can Copy the text and paste it into another text editor ET Tree Selecting this toggles the Tree Viewer on and off Utils Make ETV File Starts dialog to automatically generate an ETV or ETVX file from existing ET results This is normally not needed as all traces generated from the ET Wizard come packaged with the ETVX file ET Wizard Launches the ET Wizard to perform an Evolutionary Trace Write PyMol MolMol Macro Outputs a macro script of the current ETV state This can be saved and used as input to PyMol or MolMol This is useful when more advanced molecular viewing modes are desired based on ET results Any text output by ET Viewer utilities is viewed in the Report Viewer If the user wishes to save the output a single menu item is associated with the Report Viewer that allows the file to be saved Alternatively the user can Copy the text and paste it into another text editor Peptide Builder Inactive Will be available in future releases Help Tutorials A web based tutorial to aid the user with common ETV tasks These are also available directly from the ET Viewer website http mammoth bcm edu traceview About Provides author and v
20. r position will appear as spheres while the remainder will be shown as bonds 1 1 6 6 Residue Ranks One of the files output from the Evolutionary Trace is a ranks file This file includes the calculated rank of every alignment position from the alignment file that is input into ET Also include in this file are the structure s residue numbers and variability information Selecting Residue Ranks from the View menu will output this text file in a report viewer 1 2 Tree Viewer The Tree Viewer is utilized to view the phylogenetic tree that is associated with each Evolutionary Trace Our Tree Viewer uses code from ATV 7 to read in tree data that conforms to nhx formatting rules A modified ATV is also used to display the ET Tree The Tree Viewer is integrated with the ET Viewer and MSF Viewer When viewing integer trace results the current rank is shown on the tree by means of a vertical blue bar This bar does not appear when viewing real value traces the default since the tree does not directly correlate with the ranks rho 2 In either case examination of the underlying tree that each trace produces gives the user the ability to visualize the associations of each sequence that appear in the supplied multiple sequence alignment The presence of single branches that appear to be widely separated from the other sequences might indicate that this branch could be pruned 1 2 1 Node and sequenc
21. represents the actual results from ET Some users will however want to renumber the residues in the ranks file to match the residue numbering of an alternate structure file The ETV will not load the file unless the residue numbering of the structure and ranks file matches Users may notice that some of the rows in the ranks portion contain rather than residue numbers These are positions from the multiple sequence alignment that do not map onto the structure The final required part of the ETV file is the NHX formatted tree as output from ET Every trace has a tree file associated with it and should never be manually altered An optional addendum to ETV files is the cluster_report summary file which provides data on the z scores for each trace rank and residue This is generated automatically when each trace is run to aid the user in evaluating ET quality while viewing trace results in the ETV If for some reason the user obtains ET results that do not include an etv or etvx file ETV has a utility that will make this file automatically When used the Make ETV utility will query the user for the directory that contains the required files and concatenate them into a etv or etvx file The user should make sure that the directory contains only one each of a pss nhx file PDB file ranks file and optionally cluster_report summary file Additionally the user should ensure that these files are from the same ET otherwise the results will be
22. s a Java program and designed to be platform independent it has only been tested extensively on Windows XP machines 1 Modules The ET Viewer consists of four main modules The Structure Viewer Tree Viewer MSF Viewer and ET Wizard These modules provide closely integrated viewing of ET results and a method to modify existing traces 1 1 Structure Viewer The Structure Viewer serves as the entry point for ETV and acts as the parent application for all other content This module starts up and organizes all of the components for the GUI in their default configuration i e no molecule loaded At the top of the frame is the menu bar containing the various menu items followed by informative text describing the loaded file and ET rank statistics The majority of the frame consists of the Structure Viewer panel which displays the loaded trace results The bottom section displays text messages updating the user on file loading and descriptions of picked atoms Once an ETV file is loaded the user can move the slider to view trace results as they pertain to each rank Slider position adjusts rank and percent coverage output Percent coverage is the number of ET residues divided by the total number of residues in the structure The rank is indicated by either Rank for integer value traces or Rho for real value traces Most current traces have a statistical measure z scores associated with them to provide quality assessment of each tr
23. t structure Selecting by residue number allows the user to quickly obtain ET information on a specific residue and alleviates attempting to find the residue by clicking on the structure View Gobstopper Color Colors trace residues according to a prismatic coloring scheme Most important residues are red Least important residues are magenta Color by Cluster Trace residues are colored in order of cluster size The largest cluster is colored red Individual residues no cluster affiliation are colored black Other clusters are colored according to decreasing size as follows blue orchid green purple cyan turquoise brown coral magenta orange sky blue violet gold Segment Focus Turns off unselected atoms to allow viewing of specific residues only Background Dialog to change background color Default is black but a white background may be preferred for posters or journal figures Every other color is available as well but these are used only at the user s discretion Backbone Makes the side chain atoms invisible Bonds Shifts view mode so that the protein residues are represented as bond lines if they are not at the current rank Residues that are important at the current rank are shown as spheres Spacefill Returns view mode to spheres rather than bond lines Residue Ranks Outputs the currently open ET results ranks file to a text viewer This file lists the rank
24. unreliable 1 1 1 Mouse Control Molecule manipulation is controlled via the mouse see Table 1 The left mouse button controls protein rotation and atom picking The right mouse button controls translation On Windows computers holding the left and right mouse buttons down together will zoom the protein On other operating systems holding the left mouse button and the Alt key will provide zooming capability 1 1 2 Viewing Selection of a few different viewing modes is available via the menu bar Table 2 They are designed to aid the user in more easily identifying important residues but ETV does not have more complicated viewing options such as ribbons We do provide macro writing utilities for PyMol and MolMol to export particular rank views for further modification as desired Any text output by ET Viewer utilities is viewed in the Report Viewer If the user wishes to save the output a single menu item is associated with the Report Viewer that allows the file to be saved Alternatively the user can Copy the text and paste it into another text editor Table 1 Left Mouse button hold down Protein rotation on x and y axis Left Mouse button Click at bottom of viewing window and drag left or right Rotate protein on z axis Left Mouse button Right Mouse button Moving the mouse up or down will zoom the molecule in or out Left Mouse button Click When positioned over an atom a left mouse button c
Download Pdf Manuals
Related Search