Elaine and Alexandra, that worked, thank you J
On May 29, 2025, at 5:52 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Jacek, Your modelspec is wrong... you could try something like
combine #1 model #2
or
combine #1.1-5 model #2
Command-line specification: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>
I hope this helps, Elaine
On May 29, 2025, at 5:40 PM, Jacek Jagodzinski via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Elaine, my model panel looks somewhat different (screenshot attached). when I folloowed you example I came up with following command "combine #1.1-1.5 model #6” but it failed with message that NO structures specified. What am I doing wrong? Jacek <Screenshot 2025-05-29 at 5.37.39 PM.jpg>
On May 29, 2025, at 5:23 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Jacek, I guess what you have is five separate models (i.e. listed separately in the Models panel). You can use the "combine" command to make a new combined model from them, see:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html>
Example, if you want to make a new combined model #6 out of existing models #1-5:
combine #1-5 model #6
Of course, you'd have to modify that if you have different model numbers (look in the Models panel to make sure of what you have), and there are other options to the command that you might want to use, as described in the help link above. The example command above would keep models #1-5 in addition to the new one, but you can use the option to close them after creating the new combined model.
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 May 29, 2025, at 5:09 PM, Jacek Jagodzinski via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I am medicinal chemist. I used ChimeraX to model missing parts/loops of the protein for which I had cryo-EM structure. It is transmembrane protein consisting of 5 individual chains. I managed to reconstruct missing parts using as a template known sequences of publicly available X-ray structures of proteins and known sequences. I have now a nice assembly of five individual “repaired” proteins perfectly aligned with parts of my cryo-EM structure. However the PDB file of those FIVE individual proteins is not recognized as ONE protein with five separate chains by my other programs. I suppose there is a way to get the result I need, but I cannot find the solution by myself. Can you help?
Jacek Jagodzinski, PhD _______________________________________________ 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/
_______________________________________________ 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/