Dear Greg, I just converted my mtz file in phenix to ccp4 maps. Chimera can open the mFo-DFc.ccp4 and 2mFo-DFc.ccp4 but how to fit pdb into the map?. Somehow the map does not appear as continuous crystals as in coot. Can you please explain how to align the pdb structure wuth the map. best James
Hi James, Chimera has a Fit in Map tool (menu: Tools... Volume Data... Fit in Map) or you can use the "fitmap" command -- see the help for how to use them. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> Since this is the Chimera mailing list I answered for Chimera. However, I should mention that we are not developing Chimera any more and recommend that you use ChimeraX instead. ChimeraX is a different program, but it has the same fitting, as well as many other features and advantages that Chimera does not have. Here are some links to ChimeraX help if you decide to try that instead: <https://rbvi.ucsf.edu/chimerax/docs/user/advantages.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/fitmap.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html> Also, there is a different mailing list for ChimeraX, so if you have questions about it use the address chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> instead. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 31, 2024, at 2:05 AM, Vitali James via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Greg,
I just converted my mtz file in phenix to ccp4 maps. Chimera can open the mFo-DFc.ccp4 and 2mFo-DFc.ccp4 but how to fit pdb into the map?. Somehow the map does not appear as continuous crystals as in coot. Can you please explain how to align the pdb structure wuth the map.
best James
Hi James, I guess your atomic model already fits in the map in Coot. You can extend the map by symmetry in Chimera using the "vop cover" command. That is better than trying to fit it in the map by moving the atomic model since that won't produce the exact same position as in Coot. Tom
On Oct 31, 2024, at 8:09 AM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi James, Chimera has a Fit in Map tool (menu: Tools... Volume Data... Fit in Map) or you can use the "fitmap" command -- see the help for how to use them. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>
Since this is the Chimera mailing list I answered for Chimera. However, I should mention that we are not developing Chimera any more and recommend that you use ChimeraX instead. ChimeraX is a different program, but it has the same fitting, as well as many other features and advantages that Chimera does not have. Here are some links to ChimeraX help if you decide to try that instead: <https://rbvi.ucsf.edu/chimerax/docs/user/advantages.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/fitmap.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html>
Also, there is a different mailing list for ChimeraX, so if you have questions about it use the address chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> instead.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 31, 2024, at 2:05 AM, Vitali James via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Greg,
I just converted my mtz file in phenix to ccp4 maps. Chimera can open the mFo-DFc.ccp4 and 2mFo-DFc.ccp4 but how to fit pdb into the map?. Somehow the map does not appear as continuous crystals as in coot. Can you please explain how to align the pdb structure wuth the map.
best James
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participants (3)
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Elaine Meng -
Tom Goddard -
Vitali James