Hi Raquel, When I open your example input file in Chimera and use "write," it does save both models #0.1 and #0.2 to a single PDB file. Example commands: open model.000.00.pdb write #0 chtest.pdb ...and then chtest.pdb looks the same to me (in the 3D graphics window when I open it) as your "manually" file. It includes HELIX and SHEET records because they are automatically calculated when the input file is read, and it includes both #0.1 and #0.2 because they are submodels of #0. Technically, it is not really correct PDB format to use a single multimodel file for different proteins. The multi-model format supposed to be used for different conformations of exactly the same atoms, as in an NMR ensemble or time steps of a trajectory. However, the "write" command or the Save PDB GUI can generate this kind of file if you tell it to do so. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 15, 2023, at 3:31 PM, Raquel Cossío Ramírez via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello Chimera team,
I have been working with docking files obtained from cluspro and I'm working on a set of commands to open the files in chimera, perform a ksdssp and save them in a single individual file. The problem that I have found while doing it was that secondary structure was not well calculated for the second model, so when I run the save (write) command, I only obtain a file with 1 molecule and it does not include the MODEL 1 nor MODEL 2 header, which I need it so I can analyze it later. Here I send the code that I have been running (save_all.py) with the command and a log of the problems it present while running, as well as an example input (model.000.00.pdb) and output file (ch_model.000.00.pdb) that this code produces. Also, an example of the files that I would like to generate is included in ch_model.000.00_manually.pdb The save_all.py runs in the Ubuntu terminal as follows:
chimera --nogui save_all.py
I believe that the code could be improved by adding an option to "save multiple files in a single file" as the GUI can allow, but using the command line, I could not find that option.
I would really appreciate if you had some insight about how it could be solved. Thank you for your attention and I wait for your prompt response.
Raquel Cossío Ramírez
Corelab Genomics at Tecnológico de Monterrey <model.000.00.pdb><save_all_log.txt><save_all.py><ch_model.000.00.pdb><ch_model.000.00_manually.pdb>_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu: To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Manage subscription: