[Chimera-users] em fit refinement
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:
> 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!
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