[chimera-dev] pointers

Dougherty, Matthew T matthewd at bcm.edu
Wed Jan 1 02:38:43 PST 2014

Hi,  I am trying to track down some variables to develop some methods, and need some direction as to locations and practical options.

1) where do I find the name of the session variable?  I want to build in organizational structure for the session files and data files in regards to project management.

2) the pull down menus change depending on the dialog that is the focus.  Usually it is volume viewer and main window.  Is there a way to lock in the main viewer pull down menu? would prefer that to be constant.

3)sometimes I need to transfer a session, or receive a session from somebody.  If the session only uses pdb files I am ok.  If there are mrc files involved, then they have to be located, bundled, transferred, and linkages repaired.  I would like to get a list of all the extraneous data files that the session uses, and copy all those files into a single folder, that is usually on a thumb drive.  So I would need to develop sw to locate those files, copy them as an aggregate along with the session file.

4) for S3D, is the focal plane the same thing as the convergence plane, or is it the screen plane? Is everything that is close to the camera is negative parallax, focal plane is zero parallax, everything behind is positive parallax?

5) I have a number of related animations using different session files.  Usually I will create a core session, with the other files having small variants (eg, inclusion of different pdb or vrml files).  Each session file produces a clip, each session file has a corresponding command file that sequences the positions, and other animation components.   The end of clip1 is the beginning point for clip2, etc.  Passing positions between session files is the problem.  How do I export a position so as to import it into another session file?

6) I need to animate the lighting.  I get the impression lighting is relative to the camera, but it could be to the origin, or to the aggregate of the models, or to the clipping planes, etc.  not sure on this.  It does not appear to be saved as part of the savepos command.  I have dug into the lighting code and can move the lights around using the HID tools I am creating.   What would be the best or viable or quickest approach to animate the lights?

Matthew Dougherty
National Center for Macromolecular Imaging
Baylor College of Medicine

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