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.