[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:

In that case your map needs to have a symmetry assignment.  You may be able to add that automatically using command "measure symmetry" 

...but if that doesn't work, you could also do it manually with the "volume" command "symmetry" option:

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.

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"

I hope this helps,
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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