[Chimera-users] selections,savepos and colordef

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 4 09:57:49 PST 2012

Hi Jean-Paul,
Any named selections should already be listed in the middle bottom area of the Rapid Access interface (the startup screen), as well as in the menu: Select... Named Selections [...].  However, there is no compact way to show their definitions.

Although saved positions are not on this interface, if you restore a position and then save a scene, the scene will be shown with a thumbnail in the middle top area of Rapid Access.  Clicking the thumbnail is one way to restore that scene. Positions only include positions, whereas scenes include colors, representations etc. and are thus more accurately represented by a thumbnail image. One caveat is that saved scenes will increase session size more than saved positions, because they include much more information.

More details on Rapid Access and scenes:

I don't know of a way to retrieve a list of custom colors other than by looking in the session file, however. If you already know the name of the custom color, "colordef name" will report its color components (not the same as seeing the color, I know).   Maybe there should be a colordef option to list the names.  The problem might be in distinguishing the 169 color names that are automatically defined by Chimera from any additional ones defined by the user.

Personally I never use named selections.  Instead I use the "alias" command to create aliases and to list any previously created aliases.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 4, 2012, at 3:46 AM, Jean-Paul Armache wrote:

> Dear Chimera developers,
> I wanted to thank you for all the work that is being done on Chimera.
> It's a great software and now with the new display of the pdbs it's
> amazing.
> I was curious whether there is a way to display the saved views and
> user-defined colors in a session ? I inherited a number session files
> from a colleague and it poses a nuisance to search through the .py file
> for the names of views,selections and colors + definitions. Would it be
> possible to display it on the startup (thunderbolt icon) screen ? 
> Best regards,
> Jean-Paul

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