[Chimera-users] Recording trajectory

Eric Pettersen pett at cgl.ucsf.edu
Mon Mar 8 17:33:25 PST 2010

On Mar 8, 2010, at 11:01 AM, Francesco Pietra wrote:

> Hi:
> I am interested in following the pathway of a ligand forced to leave a
> protein. I can follow that path with the movie (NAMD format) but I
> would be interested to also have a trace of the pathway recorded. I
> would like to show around the protein the various traces for different
> pathways of exit of the same ligand.

Hi Francesco,
	One possible solution is to define a centroid at the center of your  
ligand at each frame.  Defining centroids is only available in the 1.5  
daily build.  So in MD Movie's "Per-Frame" dialog you would enter  
"define centroid ligand".  This assumes that "ligand" in fact selects  
the atoms of your ligand (and only those atoms), which you might want  
to test out beforehand with the command "sel ligand".  Otherwise you  
might have to use a more specific atom spec than "ligand".  You might  
also want to use some options on the 'define' command ("help define"  
will show those).
	This centroid path may be good enough as is, or you might want to  
show a centroid only every 5 frames or every 10 frames, in which case  
you would prefix the 'define' command with "#5:" or "#10:".
	If you want the path to be linked together rather than just a series  
of spheres, more work is necessary. You can save the series of  
centroids into a file with the "Save" button on the Axes/Planes/ 
Centroids tool.  This will give you the coordinates of the centroid  
centers.  You can then either create a BILD-format file (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html 
) or a Chimera markers file (http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#markerfiles 
).  With the former you could draw arrows, cylinders, or lines linking  
the coordinates, and with the latter you could make cylinder links  
which could then be turned into a smoothed spline path with the Volume  
Tracer tool.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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