User`s Manual v. 1.2
Contents
1. 4 10 eMap User s Manual Example of input file Comments to each line of the file Line description 50 50 100 00 2 101 c Alpha Beta Gamma 50 90 90 90 2000 0 2000 0 8000 180 Comment line abcagpy h k 1 Ampl Phase 4 11 eMap User s Manual 4 1 1 2 HKL files There are two different types of HKL files supported by eMap The first is an output from Triple2 the second is an output from TriMerge Calidris Sweden Any text file can be simply edited and then the TXT extension can be changes to HKL The format is as follows Any line starting with semi colon is treated as a comment line TriMerge file example Triple2 file example Comment SpaceGroup 4 SpaceGroup 4 Cell 42 7 41 7 73 0 90 104 6 90 KASH Radius 27 66 Cell_A 42 7 Cell_B 41 7 F hkl Cell C 73 0 ormat ap Alpha 90 Beta 104 6 0 0 1 253 3 180 Gamma 90 1 0 0 461 7 0 H K L Amp Pha 1 0 1 219 6 0 OE 55 0 1 1 326 8 75 0 0 1 253 3 180 O 0 2 875 3 0 1 0 O 461 7 0 1 0 1 219 6 0 0 1 1 326 8 75 0 0 2 875 3 0 4 12 eMap User s Manual 4 1 2 Symmetry The program will automatically jump to the next dialog Select the symmetry r Symmetry amp unit cell Symmetry r Space group L a C12 c1 may ay F Unit a 17 8965 a 90 b 17 92 B 1148 Modify c 14 328 y 90 Here you can 1 Change the space group by pressing Modify or clicking inside the2. 6 27 eMap User s Manual 6 1 2 Rotating and zooming the model Rotate the model with the mouse Press and hold the left mouse button within the 3D view area move the mouse across the screen Zoom the model using the mouse wheel or A and Z buttons on your keyboard The series of screenshots shows the sequential zooming the loaded model by the mouse wheel 6 28 eMap User s Manual 6 1 3 Model animation Model animation will set the 3D viewer in automatic rotation mode or so called animation mode Preferences gt Animation from the main menu The animation can be toggled on off Preferences Win Animatio s Animation nis ON Berge Clip planes Animatio nis OFF Preferences Win Animation Settings Clip planes Press and hold the left mouse button within the 3D view area move the mouse across the screen and release the button The model will continue to rotate in that direction Animation mode 6 29 eMap User s Manual 6 1 4 Clipping planes There is a possibility to use clipping planes which allow you to cut away a part of space in order to see in details the internal content of the map being visualized Choose Preferences gt Clip planes from the main menu or press nila on the 3D viewer toolbar The following dialog will appear Plane 3 of 6 T O Reverse normal d 30 Reciprocal hkl Real space Cartesian Real space fra
3. ri F JEI A Borra B kikuch g Prece Ready CAP NUM SCRL 18 43 44 In addition to the functions of the Reciprocal Space Viewer toolbar described above several other diffraction type visualization modes are available through the Preferences of the main menu These modes are 8 50 eMap User s Manual e 2D view Regular 2D diffraction Preferences iain sie mode default Can be controlled et scale using the Diffraction pane see 0 2D view KikuchifHOLZ lines e Kikuchi HOLZ lines Can be Rotation controlled using the Kikuchi pane Rotation animation see g 1 2 Precession Animate precession e Rotation and Rotation animation In rotation mode the electron beam is rocked back and forth in one direction or equivalently the sample is tilted back and forth in that direction It is fixed to the range 1 to 1 with 30 steps e Precession and Animate precession Can be controlled using the Precession pane see 8 1 3 Set scale allows you to scale the Oo ti lt lt i i simulated diffraction pattern exactly Scale A pix Cancel 8 51 eMap User s Manual 8 1 Working side pane dialog bars The Reciprocal space viewer offers 3 pane dialog bars on the right side default of the main view These bars can be re attached to any side of the current view or the main window left or right sides are preferable due to the vertical nature of
4. 1 26 Pha 90 1012 2023 Intensity 1 5876 etc Press J and Simulator will display the electron diffraction pattern along that zone axis 8 54 eMap User s Manual 8 1 2 The Kikuchi dialog pane Kikuchi HOL2 lines ax T gt Seat 1 Wii VAIS Convergence Kikuchi line angle mrad threshold mi 1 9 42 699 O Show disk circles O Horz lines HOLZ shift Max HOLZ index The Kikuchi dialog pane Kikuchi lines are useful for crystals with small unit cells i e lt 8 A or so Preferences Kikuchi HOL2 lines The Kikuchi dialog pane allows the user to control the disk size convergence angle the threshold for Kikuchi lines and HOLZ lines visualization mode Checking the HOLZ lines will show the central disk 000 spot enlarged NOTE in order to observe the HOLZ lines in the 000 disk the following three rules should be satisfied 1 The Ewald sphere should be switched ON i e with the frame around it 2 The calculated diffraction pattern should contain enough spots enough resolution so that the Ewald sphere can reach the upper reciprocal layers 3 The value in the Max HOLZ index 8 55 eMap User s Manual k Central beam highly magnified using x 4 should be greater than or equal to 0 default is 0 Checking unchecking the HOLZ shift will switch ON OFF the dynamical correction in the calculations of the HOLZ lines positions with
5. User s Manual IC gt M Oa UI ji G w NL July 2008 Visit our web page at www analitex com eMap User s Manual Table of Contents l SPAS cabs tes tpn EE tas sonnei ea tareaace E ee 2 3 1 1 General introduction 2 3 1 2 Support offerings 2 4 1 3 Reporting problems 2 4 2 Installationen a a N 2 5 2 1 Installation 2 5 2 2 User interface 2 6 3 Quickstart esiensini nanen n a 3 9 4 Calculation of an electron density map ss ssssesesesessseeeseee 4 10 4 1 1 Fil formats nessies toroa s 4 10 4 1 2 SYMMEtTY oaeoi noiridas ese eni E EEEa a EEE ah 4 13 4 1 3 Layers eo E AE 4 17 5 Peak Sea oseere i EA 5 20 6 BID MIB WEE iieri inn eE E AE a EE RRT E Ah 6 26 6 1 1 Th l y l Control ao scuvssvateressastannseanganseeanneevpadesannnsuaearvon 6 26 6 1 2 Rotating and zooming the model seeeseeeeeeneee 6 28 6 1 3 Model animation oe cecioas sacoreenatcuseesaee aeesscstuseecentonee 6 29 6 1 4 Chpping pl n S eee nee eee ee en eee er ny ene 6 30 6 1 5 3D view SCUINES iisdeiadaceerstarereet netewe taste eed 6 35 7 Theoretical structure factors calculation ceeeeeeeseeeteeeee 7 39 7 1 1 File form tSsssnnnn i eens 7 39 7 1 2 SYMME Y osisiiiseciisi r eiseni irus TESE EE EEEE EASKET EEEE 7 41 7 1 3 Atomic 0 1 215 8 Beene er ee ane mn eT 7 42 7 1 4 Structure factors calculation 0 eee eeeeeeeeeeseeeeeeees 7 44 8 Reciprocal Space ViGwer sjssssrcscasseccsvdebeasscaccececcsssvecsesascensstarenss 8 49 8 1 Work
6. 0 0 0 0 0 0 n aE EE EMNMMMNMNOCOCOCCCOCO Select any column to sort the reflections according to that column The first click on the column header will sort all the 7 47 eMap User s Manual reflections in descending order The second click will sort them in ascending order NOTE not available in DEMO mode It is possible to edit the data in the five columns h k l F hkl and Pha deg Double click at the cell you want to edit The other columns are not available for editing because of their dependency on these five NOTE Usually it is best to edit merged data files to keep the correct relations between symmetry related reflections Edit function is not available in DEMO mode 7 48 eMap User s Manual The reciprocal space viewer module is designed for the visualization of reciprocal space eMap Mayenite hkl HBB Eie Edt View Preferences Window Help 8 x Daca Se Ree oe EFH S COI T Aa E Start page E Mayenite hk Diffraction aX z ZONE 0 0 1 L 0 HKO 4046 8093 2023 4046 1012 2023 506 1012 253 506 126 253 63 126 0 63 4 2 0 d 2 6766 Fhkl 69 83 Pha 45 C Draw hk indices X Draw annotatic Intensity 4876 23 Convergence Voltage kv Thickne Output pane A map initialization succeeded angle 1 ile C Program Files AnalitexteMapiMayenite hkl has been loaded i
7. ADE EE Re eee n EEE E Custom colors BEEBE EE EEE EES Define Custom Colors gt gt Cancel Under basic colors you can choose the color needed If a color is missing you can define you own under Custom colors by selecting an empty square and then clicking Define Custom Colors Press OK when ready Internal and external surfaces of your model can be changed in the same way 6 1 5 2 Axes properties This dialog allows you to change the properties of the three basic axes X Y and Z and define the grids in X Y and Z planes 6 36 eMap User s Manual Visualization preferences i x Fonts and colors Grid and axes Yisualization irid and axes f Projection type Draw lines Auto grid C Line color O Show numbers C Axis color Auto scale 0 Minimum value 2 Axis weight 1 Maximum vali Toggle the plane grid ON OFF by marking unmarking Draw lines in the corresponding tab X axis Y axis or Z axis Grid ON Grid OFF Each axis is spit into 10 steps from 0 0 to 1 0 with 0 1 step by default If you would like to change this unmark Auto grid and edit Splits The default range 0 0 1 0 can also be changed Unmark Auto scale and edit the minimum and maximum values Mark Show numbers if you would like to show the numbers related to the axis 6 37 eMap User s Manual You can assign a label to each axis marking Label and inserti
8. Ma Notdefined SCY Oxidation no Isotropic parameter a Occupancy Anisotropic parameters mi 1 2 0 22 aa o ea eaf lt Back Cancel You can select a desired atom in the list under Atomic parameters Press Delete if you want to delete the atom Press Insert if you want to add a new atom to the list Press Append if you want to apply all the changes you ve done to the atomic parameters of the selected atom 7 1 3 1 Atomic position occupancy and symbol You can edit the atomic position the occupancy and the symbol or even change the element in the Atom frame The oxidation factor is not taken into the account in calculations however some file formats provide it so it can be observed in the Oxidation no edit box if available empty means 0 7 1 3 2 Temperature factors You can select the type of the temperature factor for the selected atom in the Displacement frame The following possibilities under Type 7 43 eMap User s Manual 1 Not defined All edit boxes will be disabled no temperature factor will be used during the calculations for the selected atom U anisotropic The anisotropic U temperature factor with six components is required Empty edit boxes mean 0 B anisotropic The anisotropic B temperature factor with six components is required Empty edit boxes mean 0 Beta anisotropic The anisotropic B temperature factor with six components is requi
9. even more marked broadening of the FOLZ circle Already at 0 2 precession angle the ZOLZ and FOLZ start to merge 8 59 eMap User s Manual HB cle Edt view Preferences Window Help Casas Blecoocez F s LCORL Aa t O0 kk gt Dracon Precession Pstart oestton MOUS S NG Gel ac Mel Ds On wp ee Hef Ss Me Sae i920 8 3 Symmetry determination The combined information from ZOLZ and FOLZ is very useful for symmetry determination Notice in the case of mayenite above space group 143d a 11 98 A that there are twice as many diffraction spots per unit area in the FOLZ ring than in the central ZOLZ are Notice also that the diffraction spots in the FOLZ are shifted relative those of the ZOLZ This information can be used to determine the space group as described in detail by 7 Experimentally the symmetry can be determined from such precession patterns by the program Space Group Determinator from Calidris Sollentuna Sweden An example is shown below 8 60 eMap User s Manual 8 4 Simulation of mayenite along 111 Here the symmetry is 6mm in the ZOLZ but only 3m1 in the FOLZ This excludes tetragonal and hexagonal space groups but allows trigonal and cubic space groups aax nmety zolz E HOLZ Suggestions from intensities Symm RA Symm Ra Trigonal E 2 4 95 1 0 00 3m 0001 w ubic go s ey a m 3m 111 4mm m
10. implementations of OpenGL on all available PC video cards The total number of clipping planes can be seen on the very top of the dialog it shows the text of the frame as Plane 1 of 6 where 6 is the maximum number of available clip planes in the current OpenGL release NOTE if your 3D video hardware is old and doesn t support clipping planes on the hardware level the OpenGL software implementation will clip your structure without using the hardware This can slow down the visualization during zooming or rotation 6 34 eMap User s Manual 6 1 5 3D view settings Choose from the main menu Preferences gt Settings The following dialog will appear You can choose the group of properties you would like to change in the left upper box Currently three basic setting are available to change 1 Fonts and colors 2 Grid and axes 3 Projection type Visualization preferences x Fonts and colors Visualization Grid and axes Projection type MB Background color Model colors WB Outer surface color E internal surface color Press Apply to see the changes in the 3D viewer Press OK or Cancel to leave the dialog 6 1 5 1 Colors Any color can be changed by clicking in the small colored box on the left side of the explanation text for example black for the background color This will bring up the standard Windows Select Color dialog 6 35 eMap User s Manual eT eee ADETE E LTE I
11. number You will see that the grid of the map now has 39 8 and 23 points along the x y and z directions respectively The idea of the Layer properties is to define the 3D grid in real space in order to calculate your density potential map The Start and End fractional coordinates are by default all set in the range of 0 to 1 This defines a single unit cell The program divides each range for example in the X direction EndX StartX by the corresponding number of sections for this direction SectionsX if you have selected Section number Thus you get the resolution as EndX StartX 4 18 eMap User s Manual SectionsX etc On the other hand if you define the resolution along each of X Y and Z directions the procedure is the opposite the program calculates the number of sections by EndX StartX ResolutionX Why do we need the number of sections and the resolution The number of sections defines the grid in 3D real space and eMap will calculate the value of density potential in every grid point In the above example you ll get 39 8 23 7176 points The resolution defines the grid step in real and reciprocal spaces With higher resolution the file size will grow proportionally Each grid point occupies 4 bytes in the file float data type Thus the file size is four times larger than the number of points In addition to that eMap pre calculates the same map with 1 byte size for each grid point This add
12. the Browser will assume the standard setting only 4 14 eMap User s Manual Alternatively you can browse the Tree List of space groups and select the desired space group and setting by a single mouse click Everything available in the program information about a selected space group is displayed on the right side of the Space Group Browser Press OK if you made your choice or Cancel if you don t want to change the space group Note If the space groups in the List Box and in the Tree List are not the same the one in the List Box will be used 4 1 2 2 Unit cell parameters a 39 668 alpha 90 T 7 b 8 158 beta 90 05 Cancel m 23 392 gamma 90 Restrict cell parameters to crystal system The dialog restricts the cell parameters to the crystal system by default For example a b for tetragonal and hexagonal space groups Unmark it if you have non standard space group settings and would like to change the data in disabled edit boxes 4 1 2 3 Reflections list expansion Any 3D density potential map is calculated using 3D Fourier transformation In this case the program requires a list of all 4 15 eMap User s Manual reflections After pressing Next button eMap will try to expand loaded reflections if they are unique in the file In case of large data it may take some time The expansion of reflections procedure proceeds with merging them first eMap merges all symmetry related reflecti
13. the file contains all atoms The peak list can be opened in any text editor and edited 5 25 eMap User s Manual 6 3D viewer With 3D viewer you can see the 3D map The 3D viewer module can be started from the Start page dialog using SD Here we call voxel a three dimensional analog of a two dimensional pixel 6 1 1 The level control The most important property of the 3D viewer is that you can change the threshold value and see changes in real time Press E on the 3D viewer extra toolbar The following dialog will appear Level control for 0 Al3Co 400 exp ed R Minimum Maximum 12145 97 71061 52 Threshold 29457 77 a zi Ei Surface area 6492 88 Ae cell Volume 7 20 A Joell Apply The dialog displays the minimum and maximum values found in the loaded map file The default threshold value is always half way between minimum and maximum You can change the threshold by 6 26 eMap User s Manual moving the scroll bar or editing manually the box to the right of the Threshold label 6 1 1 1 Estimate volume and surface area The dialog shows the surface area and volume above the current threshold in A and A per unit cell The surface area is approximated by triangles which fit the best to the surface with the given threshold value Summing up all the values over the given threshold and multiplying by the elementary volume of a single voxel gives the approximation of the volume
14. _int_expanded hkl I Programming Mfc E_map_2 PD3 33 hkl refls t 2 no integer txt Programming Mfc E_map_2 PD3 33 hkl refls t2 txt Programming Mfc E_map_2 test AMS 8 txt I Programming Mfc E_map_2 4cac_x_tay_3_angstt_HKL tst I Programming Mfc E_map_2 PD3 33 refls from PD 4 txt Programming Mfc E_map_2 Load Newt gt Cancel Here you can always choose a recently opened file mouse double click on the name in the Recent files column or load a new one by pressing Load NOTE Load doesn t work in the DEMO mode and will show a warning message 3 9 eMap User s Manual 4 Calculation of an electron density map You can start the module by pressing from the Start page Load a desired file or double click on a recently opened file 4 1 1 File formats eMap supports 3 different file formats right now 4 1 1 1 TXT files Any text file TXT can be simply edited The format is as follows Any line starting with semi colon is treated as a comment line Example a boc Alpha Beta Gamma this is a comment line The 1 non comment line must have the unit cell parameters separated by space s or tab s abca y Example 40 687 40 687 12 546 90 90 120 All following lines must have 5 numbers separated by space s or tab s and contain hkl Ampl Phase Here h k l are Miller indices Ampl and Phase are the corresponding structure factor amplitude and phase in degrees
15. ample 3 janisotropic temperature factor B other choices are U or T beta instead of lt B11 gt etc must be real numbers atom Ca Cal 0 30901 0 014 0 11601 aniso B lt B11 gt lt B22 gt lt B33 gt lt B12 gt lt B13 gt lt B23 gt 7 1 1 2 PDB files PDB files from the protein data bank can be used as input 7 1 1 3 CIF files CIF files can be read directly by eMap The program will search only for specific information in the file such as unit cell parameters symmetry and atomic co ordinates 7 1 1 4 INS files Shelx Shelx instruction files INS files can be read directly by eMap The program will search only for specific information in the file such as unit cell parameters symmetry and atomic parameters the same as in the case of CIF files 7 1 2 Symmetry This dialog has almost the same appearance and functions as described in 0 7 41 eMap User s Manual Theoretical structure factors calculation X Press Next gt to continue 7 1 3 Atomic parameters This dialog helps you to edit the properties of atoms available in the loaded file as well as to delete or add new atoms You can notice some relations between this dialog and the same dialog available in the Diamond program 7 42 eMap User s Manual Theoretical structure factors calculation S x Atomic parameters Atomic parameters Atom Displacement 0 of Dre kl Symbot
16. ap User s Manual above the threshold value Such a group will be treated as a single peak The following diagram can represent the pixel connection rules This picture shows a part of a map where eMap will find 9 well separated peaks on the left The threshold value is too low so there are peaks connected to each other on the right It is easy to select a desired threshold value in order to separate atoms which can be treated as peaks in the calculated 3D map The position of the peak will be determined by the position of the maximum value within the group of the grid points You can check each layer moving the scroll bar in the Layer position and coordinate frame There is a possibility to choose any projection type X Y and Z In case of big unit cell dimensions you can make a big view of the layer by pressing View This will create a special window 5 21 eMap User s Manual 15 x lt THRESH lt LAYER LAYER gt THRESH gt Layer y 0 487 Thresh 0 270 Here you can resize the window in order to enlarge the image At the same time you can change the threshold value by pressing lt THRESH decrease or THRESH gt increase on the top left Moving from one layer to another can be done using lt LAYER decrease layer number or LAYER gt increase layer number The information about the current layer and the threshold value are displayed at the top right corner When you are satis
17. box with space group name Cm 2 Change the unit cell parameters by pressing Modify You can press Next gt after expansion if needed 4 1 2 1 Space Group The Space Group Browser dialog 4 13 eMap User s Manual Space group browser EE Hermann Mauguin symbol or space group number Pe 7 a Int Tables or Equivalent No 8 e Cm 8 __j Hermann Mauguin Symbol C_m C_1_m_1 baty 8 Hall Symbol C 2y SE Schoenflies Symbol Cs 3 11m1 8 Point Group m A11 m 8 Crystal System Monoclinic B11m 8 Centrosymmetric no m 8 Centering C face centered Monoclinic axis b Bm11 8 Coordinates Cm11 8 0 0 0 142 142 0 m1 8 Symmetry Operations xl The first step in editing a space group is to specify its name or a number 1 to 230 In the upper List Box under Hermann Mauguin symbol or space group number you can put any of the mentioned and press ENTER on your keyboard The Space Group Browser will try to locate the space group by symbol or its number In case of error the Browser will notify you by a warning You must use the correct form of the name for the space group without any spaces You can use the short symbol Cm or the less ambiguous full international symbol Clm1 The full symbol allows you to specify unconventional symmetry settings For example in monoclinic space groups you can select any of a b and c as the unique axis For the space group number
18. ctional One should think about clipping planes as regular planes in their mathematical definition 3D viewer clips away everything which lies on the negative side of each clipping plane Negative or positive here is a sign given by the following equation D ne plt d 6 30 eMap User s Manual where n is the clipping plane normal the symbol means vector dot product p is any given point and d is the distance of the plane from the origin of coordinates Any point which lies on the same half of space where normal to the plane is gives positive D value The plane distance d is positive if the coordinate s origin is on the positive side of the clipping plane The origin of coordinates 0 0 0 is always in the middle of the unit cell The plane distance d is in ngstr m units The following picture shows an example of a plane a part of a plane with its normal shown as an arrow All the points on the same side as the plane normal have positive distance to the plane and negative if they are behind the plane You can design your clipping plane by editing the plane normal using three different formats 6 31 eMap User s Manual 1 Reciprocal when the plane normal components are treated as h k l indices 2 Real space Cartesian orthogonal plane normal coordinates 3 Real space fractional generally non orthogonal plane normal coordinates Any clipping plane is defined internally in eMap in
19. e right mouse button and choose Run as administrator from the context menu 2 5 eMap User s Manual Run as administrator 2 2 User interface The user interface of eMap is designed in order to achieve the principle The program drives the user Thus the most common errors and mistakes in the data handling process can be avoided Any processing module can be started from the Start page NOTE This page will only appear if the MS Internet Explorer is installed In case if eMap will failed to locate the Internet Explorer then the simplified Installed components dialog will appear 2 6 eMap User s Manual E eMap Start page Saz iD eas E Start pace kil eMap ii iE Se gdt vew preferences Window Help AnaliteX Si 0 2res edm Ca Si O 0 _3A hkl MgO hkl Aluminium hkl YBCO6 9I cif Si xml coesite 00803 hkI Crystal Structure Viewer RJ Peak search Structure factors calculator Crystallographic computing 3D viewer Reciprocal viewer Reciprocal viewer Reciprocal viewer Structure factors calculator Dynamical simulation Dynamical simulation Density potential map Density potential map 34 Reciprocal viewer Dynamical simulation Xx i Output pane Emap initialization succeeded H 4 gt bt Output ia Loading file C Documents and Settings oleynikow My Documents Structures Si 0 2r
20. es edm CAP NUM SCRL 13 47 07 The modules browser is a page with image buttons which represent each available module A short description text is displayed on the right side when you select the button using mouse In order to launch a required component click on the short description text on the right side of the corresponding image button 2 7 eMap User s Manual Installed components Density 3D viewer Structure factors potent Create picture Peak search Reciprocal viewer Multislice simulation Description Cancel The Installed components no Internet Explorer installed browser is a dialog box with image buttons which represent each available module A short description text is displayed on the right side when you select the button using mouse The modules browser can be reached by selecting the Start page tab 2 8 eMap User s Manual 3 Quick start Each processing step except 3D and reciprocal space visualizations follows a common principle having the same start dialog Density potential calculations wizard 4 x Load HKL data Recent files Folder w AINiCo hkl I Programming Mfc EMAPS PD3 33 hkl refls t2 txt I Programming Mfc EMAP w alnico_50 hkl I Programming Mfc EMAP w AINiCo hkl Programming Mfc E_map_2 su 16_ 24 hkl Programming Mfc E_map_2 PD 3_full_expanded_non integer hkl I Programming Mfc E_map_2 proi_PD 3_non
21. fied with the results close the view window and press Next The peak search dialog will open 5 22 eMap User s Manual Peak search Symmetry Peaks Min peaks distance Average atomic volume Number of atoms Results file name ProgrammingSMic EMAP w AINiCo single cell 0 2 res res lt Back Finish Cancel L_ lt Back_ Cance Here you can set up the initial data for the peak search The following possibilities can be considered during the peak search 1 The use of the asymmetric unit ASU You can mark unmark the use the asymmetric unit only in case you want to perform the search within ASU whole unit cell respectively 2 You can change the Min peak distance in ngstr m between peaks eMap removes all peaks which are too close to each other leaving the strongest peak 3 The Number of atoms is calculated by dividing the volume of the whole unit cell or ASU by the Average atomic volume default is 20 A atom This number limits the total number of peaks to be printed into an output file The program will output only the 5 23 eMap User s Manual strongest peaks when the total number of peaks found in the 3D map is greater than the Number of atoms 4 You can change the output file name or select an already existing file for overwriting The program makes the output in RES file format which can be loaded into a structure visualization program such as Diamond Pre
22. fy 6 6 46 2mm M O 3 11 22 31m 99 11 6 99 05 D 3 3 B 8 Ki Trig Cubic lt 111 gt l The systematic absences analysed in the bottom window are only compatible with rhombohedral in hexagonal setting 001 and I centered cubic along 111 8 61 eMap User s Manual 9 References 1 Z L Wang Elastic and Inelastic Scattering in Electron Diffraction and Imaging Springer 1995 476 pp 2 E J Kirkland Advanced Computing in Electron Microscopy Springer 1998 250 pp 3 R Vincent P Midgley Double conical beam rocking system for measurement of integrated electron diffraction intensities Ultramicroscopy 55 1994 271 282 4 P Oleynikov S Hovm ller X D Zou Precession electron diffraction observed and calculated intensities Ultramicroscopy 107 2007 523 533 A PDF file may be downloaded from http www fos su se svenb index html 5 P Oleynikov Exploring reciprocal space electron diffraction texture and precession Ph D thesis Stockholm University Department of Structural Chemistry 2006 90 pages 7 papers Free copies may be obtained from the author or via Anali TEX or Calidris 6 J P Morniroli A Redja mia S Nicolopoulos Contribution of electron precession to the identification of the space group from microdiffraction patterns Ultramicroscopy 107 2007 514 522 7 J P Morniroli J W Steeds Microdiffraction as a tool for crystal struct
23. in the 000 disk which leads to the so called HOLZ lines shift TeS ZONE 00 1 Uf i N L 0 HKO 3659 7319 1830 3659 915 1830 Z e 457 915 f e 229 457 b h 114 229 A K N lt 57 114 Lo RRS OY 0 57 LF Vy 24 0 d 2 6808 x Fhkl 73 92 Pha 0 Intensity 5464 17 8 56 eMap User s Manual 8 1 3 The Precession dialog pane recession Bf Diffraction FR Kikuchi ii The Precession dialog pane The Precession dialog pane allows the user to control the precession angle in Precession and Precession animation modes The min and max values of the precession angles can be changed by the user Here 0 and 3 degrees are used Animate precession allows you to follow how an electron precession pattern is built up namely by the successive summation of a large number of different electron diffraction patterns In order to see the same thing in the electron microscope the precession must be slowed down to about 1 Hz For more information about the precession technique see the home pages of NanoMEGAS at http www nanomegas com 8 57 eMap User s Manual 1 At 0 precession the electron diffraction pattern is just the normal selected area electron diffraction SAED pattern 2 As the precession angle is increased the momentary elect
24. ing side pane dialog bars 8 52 8 1 1 The Diffraction dialog pane eee eeeesseeeeeeeeeeeeees 8 53 8 1 2 The Kikuchi dialog pane c sccisssccssazcennsseececeseraccexsacess 8 55 8 1 3 The Precession dialog Panes cccissccacestvevacesescbecexesedenecexs 8 57 8 2 Simulating Precession Patterns 8 59 8 3 Symmetry determination 8 60 8 4 Simulation of mayenite along 111 8 61 9 Referentes rarna erene earnest es 9 62 2 2 eMap User s Manual 1 Preface This preface provides information about the eMap User s Manual and links to AnaliTEX technical support 1 1 General introduction eMap is a program which allows you to perform the following types or processing modules of data handling 1 Calculate an electron density from X ray diffraction or electrostatic potential from electron diffraction maps and save them in a file with special format supported by eMap Perform a peak search in the calculated three dimensional electron density electrostatic potential maps The peak positions can be saved in RES file format which can be read directly into Diamond or any other program for atomic structure visualization Visualization of calculated maps in 3D with a possibility of rotation and zooming in real time There is a possibility to add clipping planes in order to see internal details or slices of the map Calculate theoretical structure factors using tables of atomic scattering factors for X ray and electro
25. n crystallography Visualize diffraction patterns for X rays and electrons 2 3 eMap User s Manual 1 2 Support offerings You can always contact AnaliTEX by email support analitex com 1 3 Reporting problems If you can have problems running eMap or any component please report them to the AnaliTEX support team by email support analitex com eMap User s Manual 2 Installation eMap runs under Windows 2000 XP and Vista About 65MB of hard disk space is needed for the eMap program 2 1 Installation Install the program by clicking on Setup exe located in the directory eMap on the CD The program will ask you to choose destination location the default is C Program Files AnaliTEX eMap Use Browse if you want to put the program in another directory or on another drive Click Next when the program folder and drive are as required Then you will be asked to select program folders under which eMap is run from the Start menu Select the program folder default eMap and click on Finish IMPORTANT Windows Vista users and users with limited access rights may need to run eMap as Administrator for the first time For example Windows Vista has enhanced security setting Windows Vista users only using Windows Explorer locate the eMap executable under default location C Program Files AnaliTEX eMap or the destination folder chosen by the user during the installation step Click on the eMap program using th
26. ng a label text into the edit box The axis color and line color can be edited activate Line color and Axis color accordingly 6 1 5 3 3D view type The user can choose between two different projection types so called orthographic and perspective Orthographic view Perspective view With orthographic projection points with the same x and y coordinates fall exactly on top of each other when you look along the z axis With perspective projection the image looks like we would see it in real life points with the same x and y coordinates but different z will be separated Look at the corners of the unit cell as an example on the orthographic projection you see only 4 corners but in perspective projection you see all 8 corners 6 38 eMap User s Manual 7 Theoretical structure factors calculation You can calculate the theoretical structure factors for X ray or electrons using the module Theoretical structure factors The module can be started from the Start page by pressing the corresponding button A dialog with a list of recent files will appear as mentioned in the Quick start chapter see 3 Double click or press Load in order to load a file 7 1 1 File formats eMap supports 4 different file formats 7 1 1 1 TXT files or eMap file format Any text file TXT can be simply edited Any line starting with semicolon is treated as a comment line An example of an input file is presented here Exam
27. onding wavelength automatically Press Modify in the Min amp max frame if you want to modify the minimum and maximum limiting d values in Angstrom These values affect on the total number of reflections to be calculated Min amp max d values xi Min d value 0 772195 Angstrem Max d value 10 000000 Angstrem Cancel You can observe the theoretical number of reflections to be calculated in the same frame NOTE the minimum d value cannot be less then 2 where is the current wavelength 7 46 eMap User s Manual Press to calculate the theoretical structure factors The progress dialog will appear to show the state of calculations it can appear shortly for a small number of reflections Press Finish the button becomes enabled only after you did some calculations eMap will ask you to Save calculated data Here you can select a file name for the data to be saved Peak list preview You can browse the reflections list before or after expansion by pressing Preview E HKL reflections list 0 00 54 04 0 00 0 00 352 0 00 0 00 13 86 60 00 0 00 0 24 180 00 0 00 4 92 0 00 0 00 0 01 180 00 0 00 2 43 0 00 0 00 0 02 0 00 0 00 1 41 0 00 0 00 19 73 0 00 0 00 0 07 180 00 0 00 7 26 000 0 00 0 14 180 00 0 00 3 26 0 00 0 00 0 03 0 00 0 00 1 78 000 0 00 8 66 0 00 0 00 0 22 180 00 0 00 408 0 00 0 00 0 02 0 00 0 00 220 0 00 nnn nm nnn Cancel 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
28. ons if any Then expands them in order to get a full list of symmetry related reflections using the specified space group s symmetry operations However only one of the two reflections in a Friedel pair is generated so hkl is included but not Akl 4 16 eMap User s Manual 4 1 3 Layers The next step in the calculation of the density potential map is to define a 3D grid matrix using the following dialog Density potential calculations wizard Prepare grid s for calculation X interval x grid _Y grid _Z grid File name Cancel Finish Press Add to add a layer to the calculation list The 3D density potential map is calculated as a matrix of points The number of points along x y and z can be varied freely Default values correspond to the maximum resolution which depends on the outmost available reflection 4 17 eMap User s Manual Layer properties x Output file wealnico_50 name Grid size resolution dir BB Y dir 256 Zdir 256 Sections number Resolution Start and end fractional coordinates Start x 0 Endx 1 Start Y 0 End 1 Start Z 0 Endz 1 A map with uniform resolution In the example above a 39 668 A b 8 158 A c 23 392 A B 90 05 and space group Cm If you choose Resolution and type 1 in each of X dir Y dir and Z dir boxes the grid resolution becomes 1 ngstr m in all 3 directions Switch back to Sections
29. ple title Brucite source x ray wavelength CuAl min_d 0 7000 max_d 10 000000 space_group 164 unit_cell_a 3 150000 unit_cell_b 3 150000 unit_cell_c 4 770000 unit_cell_al 90 000000 7 39 eMap User s Manual unit_cell_ bt 90 000000 120 000000 unit_cell_gm atom Symb Lbl x y z OCC OXID ISO_U ANI11 AN22 AN33 AN12 AN13 AN23 atom Mg Mgl 0 000000 0 000000 0 000000 atom O 01 0 333330 0 666670 0 220500 atom H H1 0 333330 0 666670 0 418000 The format is self explanatory except maybe lines with atomic parameters Any line with atomic parameters must start with atom text and has at least first 5 non empty fields Commas must separate all fields You can leave the field empty space or tab if you want to use a default value The fields are 1 the atomic element symbol as in the Mendeleyev Periodic Table 2 the atomic label can be any text label 3 x y and z fractional coordinates of the atom 4 occupation factor assumed 1 0 if missing 5 oxidation number assumed 0 if missing 6 temperature factor In case of temperature factors see the table with examples Example 1 isotropic temperature factor B atom N N 0 30901 0 014 0 11601 1 0 0 0 iso B 23 2 7 40 eMap User s Manual Example 2 isotropic temperature factor U occupancy and oxid numbers are omitted atom N N 0 30901 0 014 0 11601 iso U 23 2 Ex
30. real space Cartesian coordinates However often it is more convenient for the user to define it in terms of reciprocal space by assigning Akl indices There are 3 clipping planes added to the Clipping planes dialog in the example n 1 0 0 d 30 n 0 1 0 d 30 and n 0 0 1 d 30 The following sequence of 3D images represents step by step addition and applying these three clipping planes 6 32 eMap User s Manual clipped away Sequentially applying 3 clipping planes a initial structure b adding 1 0 0 d 30 clipping plane c adding 0 1 0 d 30 clipping plane d adding 0 0 1 d 30 clipping plane Clipped regions marked by arrows Mark Reverse normal if the normal should be inversed You can limit the volume displayed by several planes Press Add button to add a plane into the list Press Remove to remove the selected clipping plane from the list Select a plane in the list if you want to change the value for already designed clipping plane The current 6 33 eMap User s Manual plane settings the plane normal components and the plane distance will be automatically displayed and ready to edit To after the edited values press Update Press Apply if you want to see the results of setting the clipping planes The total number of clipping planes depends on the OpenGL implementation The number of clipping planes is limited by six in all current by the year 2004
31. red Empty edit boxes mean 0 U isotropic The isotropic U temperature factor with a single component is required Empty edit box means 0 B isotropic The isotropic B temperature factor with a single component is required Empty edit box means 0 Press Append to apply the changes 7 1 4 Structure factors calculation The following dialog helps to change the source the wavelength and the limits of calculations 7 44 eMap User s Manual Theoretical structure factors calculation RS Calculate Structure Factors Wavelength Source x1ay X xray Cu Ka2 wavelength 1 54439 Calculate Min amp max Min devalue 0 7722 Max d value 10 0000 Theoretical number of reflections 372 You can change the source type in the Wavelength frame and modify the wavelength by pressing Modify Source can be X ray or electrons The X ray wavelength dialog appears if you press Modify for X ray as the Source type X ray wavelength x Source Cu v 1 544390 Radiation O Kal Kaz O Kam Cancel Here you can choose the Source type as well as the Radiation type Ka Kaz or Kam 7 45 eMap User s Manual The Electron wavelength dialog appears if you press Modify for electrons as the Source type Electron wavelength x Voltage 250000 eV Corresponding wavelength 0 021997 Here you can edit the Voltage in eV only eMap will recalculate the Corresp
32. ron diffraction pattern looks more and more misaligned Notice also that the highest resolution reflections are further out with Precession ON 3 When the precession angle is even larger the FOLZ reflections marked red here start to appear at high resolution The pink circle is centered on a small red cross at the distance corresponding to the respective tilt in degrees It is shown only when the Spot visualization mode is set to the right e s 8 58 eMap User s Manual 8 2 Simulating Precession Patterns When simulating electron Preferences window precession patterns the most clear 2D view patterns are obtained when choosing Kikuchi lines Rotation r E n Data type Fhkl and Rendering Rotation animation Precession Greyscale bg OR Animate precession For the mineral mayenite along the 011 zone axis the precession pattern at 0 precession is eMap Mayenite hki HB cie cat view Preferences Window Help Dace Ss Ble coeGur s CoL wa EE Start pace EB Mayenite hid Diffraction ax D1 Draw hk indices C Braw annotati Convergence Voltage kv Thickne angle mrad Dn tl O kk TBfoifrection Precession Mstart oestt MO ASS AG Gel Sel se 45 On we ellie Te s Me FOMOCOEVEF SS 92 Increasing the precession angle will lead to an expansion of the central ZOLZ and
33. s 25 to the file size Usually there are no problems working with files around 100 Mb except 3D viewer which is a really memory consuming module This corresponds to a map with 300x300x300 grid points GENERAL NOTES A The calculated density potential map is not normalized by the scale factor of 1 2 V where V is the volume of the unit cell The normalization factor can be added on demand B You can use non integer Miller indices hkl This is suitable for some applications such as quasicrystals 4 19 eMap User s Manual 5 Peak search The peak search finds the highest peaks in the calculated map and lists them as xyz fractional coordinates The 3D viewer can be started from the Start page using A A dialog with a list of recent files will appear as mentioned in the Quick start chapter Double click or press Load in order to load an EDM file The following dialog will appear x Threshold density value Layer position and coordinate Threshold 0 27 range 0 0 1 0 Layer 19 y 0 487179 rangeO 39 O X projection projection O Z projection Min density 64944 56 Max density 274499 274499 pe This dialog helps to choose a suitable value of the density potential threshold in the Threshold density value frame This value is critical for the peak search algorithm because it looks for groups of connected grid points in the calculated 3D map which are 5 20 eM
34. ssing Search peaks starts the peak search The progress line will run twice The first time eMap looks for peaks The second time the program processes the list of found peaks using the Number of atoms Minimum peak distance and the ASU if marked Any of these two operations can be aborted at any time pressing Abort The results of the peak search will be written into the RES file with the file name specified in the Results file name edit box In the current version eMap assigns the atomic symbol of carbon C to all atoms The peak height of a corresponding atom appears instead of the temperature factor in the output file This helps to distinguish really strong heavy atoms from light peaks TITL eMap output CELL 1 5406 8 158 12 342 14 452 90 000 90 000 90 000 ZERR 4 0 000 0 000 0 000 0 000 0 000 0 000 LATT 1 SFAC C c1 1 0 000000 0 583333 0 828571 1 70011 74 c2 1 0 500000 0 383333 0 328571 1 70011 73 c3 1 0 000000 0 883333 0 000000 1 69661 37 c4 1 0 500000 0 083333 0 500000 1 69661 37 c5 1 0 000000 0 400000 0 314286 1 68412 18 5 24 eMap User s Manual c6 1 0 500000 0 566667 0 814286 1 68412 17 c7 1 0 500000 0 783333 0 328571 1 66551 02 c8 1 0 000000 0 183333 0 828571 1 66551 02 c9 1 0 775000 0 583333 0 100000 1 64150 78 c10 1 0 275000 0 383333 0 600000 1 64150 78 When the peak search is performed over the whole unit cell eMap writes LATT 1 corresponds to the P1 space group into the output file because
35. the dialog bar items placement Any dialog pane can be closed or hidden any time by using the 2 buttons wian in the right top corner of the bar 8 52 eMap User s Manual 8 1 1 The Diffraction dialog pane The Diffraction dialog pane Diffraction allows the user to control the current zone axis indices the m zone Axis Stereographic projection view show hide the Akl Miller indices for all reflections show hide the annotation text change some parameters of the diffraction pattern such as the beam convergence angle the voltage electron diffraction and the ae ke a thickness electron diffraction verre When you move around over the stereographic projection the O Draw hkl indices X Draw annotations index h m left giv Convergence Voltage k Thickness 4 dex at the botto Sut piyes angle mrad the nearest Miller indices Left click and the stereographic I projection will be reoriented with that zone axis given at upper left at its center 0 010 200 00 33 00 3 Diffraction Kikuchi lines Precession The Diffraction dialog pane 8 53 eMap User s Manual ae Draw hkl indices does just that s PEA 03 lhipsestatios t estate ban e e fa 2 6 am N2 8 a EY p 7 foe Draw annotations toggles on off all the descriptive text on the screen 4046 8093 3 13 0 d 0 8972 2023 4046 Fhkl
36. ure identification and determination Ultramicroscopy 45 1992 219 239 8 The whole of Ultramicroscopy Vol 107 2007 issues 6 7 is devoted to the electron precession technique 9 A large number of references on electron precession can be found at the NanoMEGAS home page http www nanomegas com bibliography2 php 9 62
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