[Chimera-users] using fitmap with per-frame analysis.

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 22 09:51:27 PDT 2016


Hi Bala,
It may be possible, but it probably depends on the details of your data.

First you would try to figure out a set of commands that does what you want on a single frame.  I would just do this by entering commands manually with the trajectory open but just showing a single frame (not playing).  Once you have figured out what command(s) work on that frame, then enter them as a per-frame script in the MD Movie tool, clear the  Reply Log, and then play the trajectory with the per-frame script running from start to end without looping, then save the Reply Log contents to a file.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/reply.html>

There is a “fitmap” command to do the fitting:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>

What I imagine will be the main difficulties:

(1) figuring out what “fitmap” command options will work (or if any will work) on your data.  By default the fitting is only local, so you would need to place the atoms approximately in the right place relative to the map first.  In a non-trajectory situation this is usually just done with the mouse interactively.  However, in a less human-supervised situation such as playing through a trajectory, you may be able to use the global search “fitmap” capability, but that brings in more options and parameters.  The fitmap manual page includes a link to a video tutorial on global searching:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#global> 

(2) be aware that the fitting depends on the displayed contour level of the map unless you specify “envelope false”.  Contour level can be adjusted manually in the Volume Viewer dialog or with the “volume” command.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general>

(3) there will be several lines of output per frame, so you may want to include a command in the per-frame script to echo frame number to the Reply Log so it will be easier to figure out which info goes with which frame.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/echo.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Mar 21, 2016, at 9:45 AM, Bala subramanian <bala.biophysics at gmail.com> wrote:
> 
> Friends,
> I have a task which is as follows; I have done the simulation of a protein, whose EM map is already available. 
> 
> I want to fit the MD snapshots on to the map and to filter out some best frames based on the overlap statistics. I am aware that chimera does only rigid body fitting. 
> 
> I would like to know, for instance, if I can open the EM-map and the MD traj in Chimera and use per-frame analysis to achieve my goal. Also, i need some way to output/write the fitting statistics (eg. overlap value) to a file so that i can later filter out the best frames based on the statistics.
> 
> Thank you,
> Bala



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