Elaine - You are great! I just responded to your other mail too. I think I found the problem and it was/is my user error. I was doing a late night on this and must have accidently moved my reference before saving. Didn’t catch it this morning. Sorry about that waste of time. Thank again for all your help over these many years! Jim _____________________ James Nettles, PhD nettlesconsulting@gmail.com +01.404.966.4617
On Apr 11, 2025, at 1:18 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Oops, I guess the other message I just responded to was about this same thing? I got confused since you sent a separate message.
Anyway, I was not able to reproduce this problem. Although you used the Model Panel function, it brings up the same dialog as File... Save PDB in the main menu. I fitted two structures and saved the fitted one relative to the other using the Model Panel function and the resulting save dialog. Then when I reopened both, they were in the correct spatial relationship. Tested in Chimera 1.18 but I don't think any of this functionality has been changed for a long time.
All I can say is to make sure you are saving the models relative to each other, which is specified in the save dialog (not the Model Panel), but it sounds like you were doing that already.
You could also try saving 1zh1 relative to itself right after saving your model relative to 1zh1 and then opening both of those newly saved models... but it really shouldn't be needed and I don't see how it would give a different result.
Regards, 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 11, 2025, at 8:51 AM, James Nettles via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello,
I have built a Chimera model of N-term and C-term folding associated with a particular dimeric crystal structure associated with HCV.
The crystal structure (1zh1) is our reference and we identified theoretical low-energy folds that correlate well with our biological data. We want to be able to upload pdb’s of our folding models with the data presented in the paper so that readers can also see the interactions in 3D.
I used the writePDB function and chose to Save relative to 1zh1 in Model Panel, but the results come out misaligned.
I’m obviously doing something wrong, have tried various things but have not been able to figure this out.
Any tips?
Thanks,
Jim _____________________ James Nettles, PhD nettlesconsulting@gmail.com +01.404.966.4617
<1zh1_NandCfolds.png><pdb_write Fit_error.png>
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