[Chimera-users] em fit refinement

Feixia fvy2 at unh.edu
Mon Jan 14 20:36:04 PST 2013

It is good.  Thank you so much, Elaine!


On Mon, 14 Jan 2013 20:33:10 -0500, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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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