Save PDBs relative to each other
On Apr 11, 2025, at 9:35 AM, James Nettles <nettlesconsulting@gmail.com> wrote:
Hi Elaine, I tried submitting a new question to the list, but received a response that I’m not a list member.
I am trying to output some models in PDB format and am having problems getting the coordinates of the sports to align properly when read back in.
I haven’t been able to figure what I'm doing wrong.
Your help will be appreciated.
Jim
Hi Jim, That message is probably caused by sending the message from a different address than what is signed up to the list. If so, your question has to be approved by the moderator (not me) but usually it is within a day. Otherwise we would be inundated with spam messages from addresses that aren't list members. Re your question: If you moved one model relative to the other and want to maintain their relationship, you need to use the save "relative" option. Doesn't matter which model is relative to which, as long as they are all relative to the same model. This is in both the File... Save dialog and the "write" command. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> These are the address for managing list subscriptions (Chimera and ChimeraX users) <https://mail.cgl.ucsf.edu/mailman/mailman3/lists/chimera-users.cgl.ucsf.edu/> <https://mail.cgl.ucsf.edu/mailman/mailman3/lists/chimerax-users.cgl.ucsf.edu...> ChimeraX has an analogous relative saving option for PDB files in both the File... Save dialog and the "save" command (instead of Chimera's "write" command). 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
Hi Elaine, thanks for the response. I though I was registered with this address, but I may be wrong. I certainly understand the need to filter spam. Regarding my question - I may have figure it out. It looks like I may have accidentally shifted the reference coordinates in a late-night save. I just pulled in new reference coordinates from the PDB and the alignments now seem to be working. Next step is to attempt a Morph-movie unfolding from the crystallographic coordinates to the biological relevant one. You may hear from me again ;-) I love Chimera and look forward to trying X on a newer machine. Thanks again! Jim _____________________ James Nettles, PhD nettlesconsulting@gmail.com +01.404.966.4617
On Apr 11, 2025, at 1:00 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
On Apr 11, 2025, at 9:35 AM, James Nettles <nettlesconsulting@gmail.com> wrote:
Hi Elaine, I tried submitting a new question to the list, but received a response that I’m not a list member.
I am trying to output some models in PDB format and am having problems getting the coordinates of the sports to align properly when read back in.
I haven’t been able to figure what I'm doing wrong.
Your help will be appreciated.
Jim
Hi Jim, That message is probably caused by sending the message from a different address than what is signed up to the list. If so, your question has to be approved by the moderator (not me) but usually it is within a day. Otherwise we would be inundated with spam messages from addresses that aren't list members.
Re your question: If you moved one model relative to the other and want to maintain their relationship, you need to use the save "relative" option. Doesn't matter which model is relative to which, as long as they are all relative to the same model. This is in both the File... Save dialog and the "write" command. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
These are the address for managing list subscriptions (Chimera and ChimeraX users) <https://mail.cgl.ucsf.edu/mailman/mailman3/lists/chimera-users.cgl.ucsf.edu/> <https://mail.cgl.ucsf.edu/mailman/mailman3/lists/chimerax-users.cgl.ucsf.edu...>
ChimeraX has an analogous relative saving option for PDB files in both the File... Save dialog and the "save" command (instead of Chimera's "write" command).
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
participants (2)
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Elaine Meng -
James Nettles