Hi Julius, There is no command equivalent for that part of Render By Attribute unfortunately. I've put making a command equivalent on a to-do list. So you will have to resort to the Python part of the per-frame scripting dialog. I've attached a Python file that goes through currently open molecules and writes out the areaSAS attribute of residues into files named /var/tmp/sasNNN where NNN is 001 for frame 1, 002 for frame 2, etc. You will of course have to have added a surface. You can use the "Insert text file..." button of the per- frame dialog to directly enter the script from the file. If you know Python, the script is pretty straightforward. The only tricky part is right at the beginning where it calls checkForChanges(). This allows the surface-computation code to immediately notice that the structure coordinates have changed and recompute the surface. Otherwise, the surface-computation code wouldn't get that notification until after the per-frame script had run, so the surface areas we print out would always be off by one frame. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 5, 2009, at 7:52 AM, Julius Su wrote:
Hello,
Does anyone know what script command could be used to output an "attribute assignment file" in Chimera, specifically for the areaSAS attribute?
I am trying to show how the solvent accessible surface area on various residues changes over the frames of a multitrajectory PDB file. To do this I am trying to write a small script in "MD movie" that computes the solvent accessible surface for each frame, then outputs the areaSAS values.
I was previously able to do this by loading in all the PDB geometries at once, then using the "Render attributes by ..." dialog, but this method does not scale well to very large proteins (the program runs out of memory trying to compute all the surfaces at once). Thus I am trying to do this task sequentially with a script.
Thanks much!
Julius _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users