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I have to convert 13000 all atom pdb files into files with c-alpha only. Is there any way i can convert all the files in one go using pymol??... Though i can convert each and every file but it will be quite tedious.

asked Jun 10 '12 at 22:16

Tasneem%20Ali's gravatar image

Tasneem Ali

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Do I understand it correctly that you only want to retain the CA atom information from your original PDB file? In that case I would simply use some Linux shell scripting to select only the CA entries in the original PDB file.

For one PDB file that would work like: grep ATOM "pdbfile" | grep CA

that will give you the output on the screen; you can redirect this to a new file by doing: grep ATOM "pdbfile" | grep CA > "filename"

If that gives the result you want, you simply have to loop over all your 13000 files and that's it... I think that is an easier solution than using PyMol, but I am sure you can do it in there as well (probably somehow via the Python shell scripting). Is there a specific reason you want to use PyMol for this purpose?


answered Jun 13 '12 at 16:03

renee's gravatar image


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