One correction: The PDB file saved from DMM.cif in ChimeraX (DMM.pdb attached) only has chain A. The other file (extra.cif) is the one with the many chains starting with Aa. But the main point is that the saved PDB file works for matchmaker. Elaine
On Mar 23, 2025, at 9:08 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Thanks, Dan! Hi Javier,
Yes, when you open DMM.cif in ChimeraX. the Log says it is missing the entity information. From the graphics window I can see it does not generate chains, only a bunch of dots.
<Screenshot 2025-03-23 at 9.02.03 AM.png>
You can also save the DMM.cif in ChimeraX as a PDB file, close and reopen it from the PDB file (which shows in the Log that several chains starting with Aa were detected) and then use matchmaker.
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 Mar 23, 2025, at 8:04 AM, Daniel Grba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Javier,
To me, it looks like ChimeraX is having a bit of trouble with the Kihara (DeepMainmast?) file (DMM.cif). Opening it in PyMol and resaving the CIF file seems to then make it recognisable for ChimeraX and subsequent matchmaker jobs.
Hope this helps, Dan
On 23 Mar 2025, at 14:09, Javier Sánchez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
.cif files
El dom, 23 mar 2025 a las 15:08, Javier via ChimeraX-users (<chimerax-users@cgl.ucsf.edu>) escribió: I would upload the two .cif files, but I don't see the option to upload files in the webpage