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ShelXle : A cute GUI for SHELXL

ShelXle : A cute GUI for SHELXL. Christian B. Hübschle 17.11.2011. Outline. Main Features Editor OpenGL representation of the structure Electron-density maps Customization Renaming Function Convenient Functions New Functions Plans.

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ShelXle : A cute GUI for SHELXL

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  1. ShelXle: A cute GUI for SHELXL Christian B. Hübschle 17.11.2011

  2. Outline • Main Features • Editor • OpenGL representation of the structure • Electron-density maps • Customization • Renaming Function • Convenient Functions • New Functions • Plans J. Appl. Cryst., 44, (2011) 1281-1284.

  3. The paper is published!J. Appl. Cryst.,44, (2011) 1281-1284. J. Appl. Cryst., 44, (2011) 1281-1284.

  4. The GUI J. Appl. Cryst., 44, (2011) 1281-1284.

  5. The GUI File Tool Bar Selection Tool Bar Editor Tool Bar Extra Tool Bar View Tool Bar Status Bar J. Appl. Cryst., 44, (2011) 1281-1284.

  6. The GUI Information Window OpenGL view Refinement History Q-Peak Legend Rename Mode Editor window J. Appl. Cryst., 44, (2011) 1281-1284.

  7. The Editor Hide Button Float Button Part selector Residue selector Cursor Position J. Appl. Cryst., 44, (2011) 1281-1284.

  8. The Editor Line number area Code completer J. Appl. Cryst., 44, (2011) 1281-1284.

  9. The Editor AFIX Highlighter Current Line Indicator Part Highlighter Error Indicator J. Appl. Cryst., 44, (2011) 1281-1284.

  10. The Editor Context Menu J. Appl. Cryst., 44, (2011) 1281-1284.

  11. The Editor Search and Replace • Regular Expressions • Highlighting of Hits • [Ctrl+F] or [F3] Tooltip on mouse over J. Appl. Cryst., 44, (2011) 1281-1284.

  12. The Editor Tooltip on mouse over J. Appl. Cryst., 44, (2011) 1281-1284.

  13. The OpenGL View J. Appl. Cryst., 44, (2011) 1281-1284.

  14. The OpenGL View This atom is selected The mouse is over O3 in Residue 2 J. Appl. Cryst., 44, (2011) 1281-1284.

  15. The OpenGL View Select multiple atoms by pressing [Ctrl]+left click J. Appl. Cryst., 44, (2011) 1281-1284.

  16. The Selection Tool Bar Hides Information Window, Refinement History and Editor Shows molecular graphics with central or orthographic Projection Completes molecules in the asymmetric unit Adds a Centroid Dummy atom Shows the asymmetric unit only Sets rotation center to selected atom(s) Enters/Exit Rename Mode Hides everything not selected Shows/Hide Q-Peak Legend Hides H-atoms Draws lines between Q-Peaks Connects the two selected atoms Indicates hidden objects Disconnects the two selected atoms Hides PART –N Ghosts Deselects the selected atoms Highlights atoms in Parts Kills selected atoms [Ctrl]+[Del] J. Appl. Cryst., 44, (2011) 1281-1284.

  17. Context Menu by right click on atom J. Appl. Cryst., 44, (2011) 1281-1284.

  18. Electron-Density Maps Defines how dense the lines are drawn (critical for speed) [Ctrl]+ Mouse wheel changes [Shift]+ Mouse wheel changes Blue mesh: Observed data with model phases J. Appl. Cryst., 44, (2011) 1281-1284. Red andgreenMesh: Observed data minus model green+red-

  19. Customization • Tool bars can be moved to different places • Sub windows can be detached and moved to different places. If a sub window is moved over a existing one the windows get stacked and a tab appears to bring one of them in front. Grab here with the mouse and drag around. J. Appl. Cryst., 44, (2011) 1281-1284.

  20. Customization • The Q-Peak Legend can’t be moved. • The Selection Toolbar has no grab area, but in the Settings menu it can be configured. J. Appl. Cryst., 44, (2011) 1281-1284.

  21. Customization Right clicking on the menu or any tool bar shows this menu. Here any hidden tool bar or window can be recovered. When Rename Mode is visible you are in Rename Mode and vice versa. J. Appl. Cryst., 44, (2011) 1281-1284.

  22. Customization -External Programs Detached program run independently from ShelXle for others a dialog box with output is provided. J. Appl. Cryst., 44, (2011) 1281-1284.

  23. Customizing –View Menu Toggles fog. Fog density by [Alt + Mouse wheel] Cuts out a wedge from the front side of the OpenGL View so that the inside of a complicated structure becomes visible (currently only with central perspective) J. Appl. Cryst., 44, (2011) 1281-1284.

  24. Atom-Styles Dialog J. Appl. Cryst., 44, (2011) 1281-1284.

  25. Atom-Styles Dialog Intersect. Planes+ Surface Principal ellipses2 Intersect. planes2 Intersect. planes Play around with Checkboxes to figure out what you like best! Uni color bonds Dashed bonds to o No ADP J. Appl. Cryst., 44, (2011) 1281-1284.

  26. Rename Mode J. Appl. Cryst., 44, (2011) 1281-1284.

  27. Rename Mode J. Appl. Cryst., 44, (2011) 1281-1284.

  28. Rename Mode Residue Class can only be edited if ResiNr is not yet in use. n can vary from 2 to N+1. With N the number of existing Free Variables. If there is one unused in between n can also not be greater. If the Label number is -1 no Number is used in the Label. If Scattering factor is “any” then no check of usage of that Label can be done. J. Appl. Cryst., 44, (2011) 1281-1284.

  29. Convenient Functions • asks before saving. • no questions, inserts ANIS instruction • List viewer with syntax highlighting and search function [Ctrl+F] • moves fragments into unit cell box close to the origin. No “uniq” of symmetry disassembled molecules. Use “move … here” in context menu J. Appl. Cryst., 44, (2011) 1281-1284.

  30. Convenient Functions is only present when atoms with refined Uijs are present. “create Q-Peaks from Fo-Fc map” is useful if density close to existing atoms is present. J. Appl. Cryst., 44, (2011) 1281-1284.

  31. Convenient Functions adds H-atoms including corresponding AFIX instructions. If electron-density maps are calculated the position of methyl H-atoms is optimized and hydrogens in O-H…contacts (excluding water) are generated. Increasing map precision might help. Repeated usage might find more H’s Only available on freshly loaded or saved files! J. Appl. Cryst., 44, (2011) 1281-1284.

  32. Convenient Functions Inverting structure changes the space group if enantiomorphic. Origin is moved if necessary but move in cell might then be necessary Use before and after! J. Appl. Cryst., 44, (2011) 1281-1284.

  33. Example: Solved Structure in P1 which is P-1 Select pairs of chemical identical atoms and click on J. Appl. Cryst., 44, (2011) 1281-1284.

  34. Example: Solved Structure in P1 which is P-1 Select pairs of chemical identical atoms and click on If the bonds cross each other in one point then structure is P-1! J. Appl. Cryst., 44, (2011) 1281-1284.

  35. Example: Solved Structure in P1 which is P-1 Select pairs of chemical identical atoms and click on If the bonds cross each other in one point then structure is P-1! Select all or at least one pair of chemical identical atoms and click on J. Appl. Cryst., 44, (2011) 1281-1284.

  36. Example: Solved Structure in P1 which is P-1 Select all or at least one pair of chemical identical atoms and click on J. Appl. Cryst., 44, (2011) 1281-1284.

  37. Example: Solved Structure in P1 which is P-1 Select all or at least one pair of chemical identical atoms and click on Select coordinates of the Cnt1 and copy to clipboard Type in MOVE and paste the coordinates Change the sign of the coordinates and add 1 J. Appl. Cryst., 44, (2011) 1281-1284.

  38. Example: Solved Structure in P1 which is P-1 Change the sign of the coordinates and add 1 Save and refine. The Centroid dummy atom should no be at the origin. Select the no longer needed fragment and delete them. Delete the centroid dummy if you want Change LATT -1 into LATT 1 and save + refine. J. Appl. Cryst., 44, (2011) 1281-1284.

  39. Example: Solved Structure in P1 which is P-1 Change the sign of the coordinates and add 1 Save and refine. The Centroid dummy atom should no be at the origin. Select the no longer needed fragment and delete them. Delete the Centroiddummy if you want Change LATT -1 into LATT 1 and save + refine. J. Appl. Cryst., 44, (2011) 1281-1284.

  40. Symmetry manager J. Appl. Cryst., 44, (2011) 1281-1284.

  41. Symmetry manager J. Appl. Cryst., 44, (2011) 1281-1284.

  42. ENVI J. Appl. Cryst., 44, (2011) 1281-1284.

  43. Part Highlighting J. Appl. Cryst., 44, (2011) 1281-1284.

  44. Plans: • DISP from wavelength • FREE and BIND instructions in file after clicking these functions in Selection Tool Bar • Help! FAQ, more Videos. • Linux distributions • More sort options • ENVI with graphics • …getting cited. J. Appl. Cryst., 44, (2011) 1281-1284.

  45. Credits • George M Sheldrick, • BirgerDittrich, Kevin Pröpper, Julian Holstein, • Krzysztof Radacki, Håkon Hope, Daniel Kratzert Joseph H. Reibenspies, Frederik J Holander and many other testers and users. • Thank YOU! • (yesterday 16:00 2031 downloads!) J. Appl. Cryst., 44, (2011) 1281-1284.

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