[Chimera-users] script command for writing out areaSAS attribute?

Eric Pettersen pett at cgl.ucsf.edu
Thu Feb 5 11:20:40 PST 2009

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 Pettersen
                         UCSF Computer Graphics Lab

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 at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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