[Chimera-users] Using per-frame scripts with color by attribute/bfactor

Eric Pettersen pett at cgl.ucsf.edu
Tue Mar 24 11:42:25 PDT 2009

Hi Andrew,
	At this point the only data that Chimera supports on a per-frame  
basis is atomic coordinates.  So there is only one bfactor per atom,  
not one bfactor per atom per frame.  The only way around this that I  
can think of is to not to overload the bfactor field but to instead  
put your per-frame data into a series of attribute assignment files  
that you would read in with the defattr command at every frame.  You  
could then use your rangecolor command after that (with whatever  
attribute name you used in the assignment file).
	I believe VMD supports per-frame data, if that is of any help.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Mar 24, 2009, at 11:15 AM, Andrew M. Simms wrote:

> I am making some MD movies using the multiple-pdb file format.  I am  
> using coloring by attribute, in this case overriding the “bfactor”  
> attribute for my own purposes.  The nature of my analysis is such  
> that the bfactor can change from frame to frame.  I use this command  
> in the per-frame script:
> rangecolor bfactor,a min white max green
> However, when I try to make a movie, it appears that the bfactor  
> attribute changes are not reflected in the animation.  If I look at  
> generated structures individually they are fine.
> Is there something special I need to specify in per-frame script?
> Thanks!
> --Andrew
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