[Chimera-users] Recording trajectory

Eric Pettersen pett at cgl.ucsf.edu
Tue Mar 9 14:45:12 PST 2010

On Mar 9, 2010, at 2:17 PM, Francesco Pietra wrote:

> Hello Eric:
> I have seen your later correction mail.
> I had a bad day, that is little time for chimera and with little
> success. Please try to guess were I was faulty.
> francesco at tya64:~$ chimera --version
> chimera alpha version 1.5 (build 30193) 2010-03-06 09:27:34 GMT
> francesco at tya64:~$
> This is amd64, at the moment I have no 32bit computer.
> <select ligand> selects too much.
> <select :residue.number>
> <select :residue.name>
> do select exactly what I want (which is a small ligand of HEME ligand
> of the protein.
> The problem was with <define> command
> MD-movie...Per-Frame "define centroid :residue.number" ... Apply
> then activating the movie gave the same view as not going through the
> Per_Frame, i.e., the small ligand does not leave any sphere on the
> path. I did not investigate if the sphere are too small to be seen at
> the magnification I used, ore have the same color as the background
> (black). Very likely, I did some other major mistake.

Not sure what to say.  Works for me.  I've appended an image of  
centroids tracing the motion of a small ligand in an RNA binding  
site.  I used a step size of 10 and this 'define' command:

define centroid raiseTool false radius 1.0 color goldenrod sel

"raiseTool false" prevents 'define' from trying to bring up the Axes/ 
Planes/Centroids tool (and update that tool's table) for every  
centroid created.  The other options control the size and color of the  
centroid.  I had the small ligand selected so 'sel' is my atom spec.   
I tried it a second time with ":35" (which also selects the small  
ligand) and that worked too.

FYI, "~define" will get rid of all the centroids.

I hope this helps somehow.  Are you sure you had the "Interpret script  
as" part of the per-frame dialog set to "Chimera commands"?  I can't  
imagine that you didn't, since you would have gotten some kind of  
error if it had been interpreted as Python.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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