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User Guide

  1. Files
  2. Control Panel
  3. Move & Rotate
  4. Display
  5. Rendering
  6. Tools
  7. Mutations
  8. Torsions
  9. Preferences
  10. hardware stereo
  11. electrostatics
  12. surface
  13. tips & tricks

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by N.Guex
& T.Schwede

 

 

 

 

 

 

Cool Features

This page can be considered as a collection of tricks and tips that didn't fit well in other pages. Even though the Swiss-PdbViewer is quite intuitive, some nice features are more burried. Therefore reading this page will transform you in a Swiss-PdbViewer guru.

  • "option" click on a group name (right mouse button on the PC) either in the control panel or in the align window will center the carbon alpha of the group in the display window. It is quite useful if the group was out of screen, and can also be used to rotate the molecule around the carbon alpha (see the paragraph about the rotation tool ).

 

  • Hitting the "Help" key or the "=" key ("Insert" key or right mouse button for PC users) will automatically move and scale the molecule so that all visible groups fit in the view.

 

  • "Shift" click on any column of the control panel apply the change on all groups. For example, shift-click in the "side" column will display/undisplay all sidechains, shift click in the "color" column will prompt for a new color to apply to all groups...

 

  • You can go directly to the top or the bottom of the Control Panel, Align Window or Text Window with the keyboard "Page-up" and "Page-down" keys (nothing exceptionnal here).

     

  • When slab mode is activated, its position along the Z axis can be changed by holding down the shift key while moving the mouse up or down. It allows to look at different parts of the protein.

 

  • It is possible to renumber amino-acids by selecting them and then using the "Rename Current Layer" item of the Edit menu. You will be asked for a number that will be applied to the first amino-acid selected. Next selected amino-acids wil be renumbered accordingly.

 

  • You can change the dot density in the dialog that allows to change the windows caracteristics (size, view angle, and so on).
    Please, note that dot surfaces are recomputed after any operation, and it can take time (however, you may interrupt the process any time by hitting the "esc" key). The reason I do not store all computed points and then rotate them is purely a memory concern (some programmers have to take care of the few memory that remains once you have opened a word processor and a web browser).
    Note that you can momentaneously prevent all dots surface to be drawn even if they are marked "on" in the Control Panel with an option of the "Display" menu.

     

  • Holding the shift key while choosing any of the "Color By" item of the display menu will apply changes to all layers.

  • Holding the Control key while choosing any of the "Color By" item of the display menu will apply changes to selected groups only.

  • Holding the shift key while selecting an amino-acid in the "Align window also selects corresponding aa of other layers.

     

  • Hitting the "*" key while the mouse is on-top of an aa in the align window will browse the rotamer library to select the best sidechain.

  • Clicking on an ATOM or HETATM line of a text pdb file will automatically center the view on the clicked atom and display only groups that are in a 7Å sphere around this atom.

  • Clicking on a CRYST1 line of a text pdb file will load the unit cell infos (The unit cell is displayed only when the appropriate checkbox item of the EDM preferences is enabled).

  • Clicking on a MTRX line of a pdb file will load the matrix transformation and will let you apply it on the currently selected groups of the current layer.

  • Clicking on a line of a text file containing an uppercase amino acid name followed by a number will automatically center the view around this residue (provided that such a group exists in the current layer). This is very useful to inspect results of whatcheck [4].

  • Left and right arrow keys will center the view around the CA of the following (or previous) residue when an electron density map is loaded.

  • up and down arrow keys will change the sigma contouring value when an electron density map is loaded. (for the second contouring value, use shift key).