Hello, I am trying to use matchmaker command (matchmaker #1 to #2 showAlignment true) with two cif files I've obtained from Kihara and Modelangelo. The problem is that, once I try to use the matchmaker command, I obtain the following error: "No matrix compatible with both reference structure and all match structures" and I don't know what is failing. Is it because the two structures are too different from each other? I hope I can get more information about this error message Thank you in advance, Javier
I would upload the two .cif files, but I don't see the option to upload files in the webpage
.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 _______________________________________________ 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/
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<mailto: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<mailto: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 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ <DMM.cif><extra.cif>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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. 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
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
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