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
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.


_______________________________________________
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu
To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu
Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/