How to effectively process multiple .pdb files?

[zyang20]

Hi all, does anyone know how to do a batch processing of multiple .pdb files? the web server only allows one at a time.
Thanks

[sobolevnrm]

I would recommend downloading the PB2PQR binary with pip install pdb2pqr and using that.

[zyang20]

I did that in Jupyer notebook. But I couldn't figure out how to launch the software. There are no clear instructions. Anyone could give me instructions step by step? Thanks a lot.

[sobolevnrm]

Pip installs the command-line program pdb2pqr30 that you can use to run PDB2PQR--that is the preferred mode of execution (not via a notebook). However, pip also installs the pdb2pqr module from which you could import main_driver and manually pass the desired argument namespace returned by build_parser.

I'm going to convert this issue to a discussion since others may have the same question.

[zyang20]

Thanks sobolevnrm for the reply. Actually I did 'pip install pdb2pqr' using the terminal launched from Annaconda (this was Windows 10). I will give it a try in Mac or Linux terminal. Thanks