[Chimera-users] em fit refinement

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 14 17:33:10 PST 2013


Hi Feixia,
Tom is away from work for a couple weeks.  In the meantime, I'll try to point you in the right direction...

See the symmetric fitting option of command "fitmap" and example video:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#symmetric>
<http://www.cgl.ucsf.edu/chimera/videodoc/SymFitDNAb/>

In that case your map needs to have a symmetry assignment.  You may be able to add that automatically using command "measure symmetry" 
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry>

...but if that doesn't work, you could also do it manually with the "volume" command "symmetry" option:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#symmetry>

The sequential fitting might also be useful for you, but you can't do it at the same time as symmetric fitting.  There is also an example video of that.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#sequence>
<http://www.cgl.ucsf.edu/chimera/videodoc/FitSeq/>

For setting the level, I am no expert, but I thought for some purposes, people use a level to produce a surface-enclosed volume that gives a reasonable density (protein mass is known).  You could measure the isosurface-enclosed volume, for example with "measure volume"
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#volume>

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 Jan 14, 2013, at 2:38 PM, Feixia wrote:

> Hi Tom,
> I have a question about multiple fit.  Essentially, I have a map of a dimer.  For each monomer, I have three domains.  I have built models for each of the domain.  I tried to fit each individual domain into the map, but found the same domain taking different orientations in different monomer, so I can't achieve 2-fold symmetry.  I wonder what would be a sensible approach to fit.  Also, what would be a good value to select for 'level' for the map.  The map is from negative-staining data with 18A resolution.  Thanks a lot!
> Best,
> Feixia




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