How can I overlay the 2Fo-Fc density map onto the amino acid residues I specified?
Every time I open the map file in ChimeraX, I find that it doesn't overlap with my PDB structure. Why is this the case, and how can I make them match? Thank you for your attention. I'm looking forward to your reply.
Without knowing your exact data, I can only guess that maybe the "volume cover" command is what you need. see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#cover> 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 Apr 24, 2025, at 2:26 AM, 1025049892--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Every time I open the map file in ChimeraX, I find that it doesn't overlap with my PDB structure. Why is this the case, and how can I make them match?
Thank you for your attention. I'm looking forward to your reply.
For X-ray data, usually it could be the conversion from mtz to ccp4/map format, one loses the origin of a reference is not given. Make sure to convert with the pdb as an input if using a tool in say Phenix (mtz2map) as a reference. When you open the ccp4/map format map it should be aligned with the pdb Sent from Outlook for iOS<https://aka.ms/o0ukef> ________________________________ From: Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Thursday, April 24, 2025 5:58:37 PM To: 1025049892@qq.com <1025049892@qq.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: How can I overlay the 2Fo-Fc density map onto the amino acid residues I specified? Without knowing your exact data, I can only guess that maybe the "volume cover" command is what you need. see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#cover> 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 Apr 24, 2025, at 2:26 AM, 1025049892--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Every time I open the map file in ChimeraX, I find that it doesn't overlap with my PDB structure. Why is this the case, and how can I make them match?
Thank you for your attention. I'm looking forward to your reply.
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Kelvin Lau