Re: [Chimera-users] em fit refinement
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 -- Feixia Chu, Ph.D. Assistant Professor Biochemistry Graduate Program Coordinator Molecular, Cellular & Biomedical Sciences University of New Hampshire Gregg Hall, Rm436 35 Colovos Rd Durham, NH 03824 Tel 603 862 2436
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
It is good. Thank you so much, Elaine! Best, Feixia On Mon, 14 Jan 2013 20:33:10 -0500, Elaine Meng <meng@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
participants (2)
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Elaine Meng -
Feixia