We have a docking target protein with multiple chains (A,B and C). However, I just need chain A. How can I delete the 2 other chains from the docking target protein.
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$\begingroup$ Hi @ibio_rep1, sorry to be persistent but please remember to accept one of the answers below. I didn't know about the pdb tools and its useful trick to know. It is important for the momentum of the site. Both respondees are serious structural bioinformaticians. $\endgroup$– M__ ♦Commented Aug 17, 2020 at 17:03
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2 Answers
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If the tag r is incorrect, the easiest way is to download and install PyMOL: https://pymol.org/2/
Drap and drop your pdb file and type remove not chain A.
Then save molecule via the menu as pdb or type save some_file_name.pdb (will be in your home root folder).
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$\begingroup$ Thank you for the help. Appreciate it. $\endgroup$ Commented Aug 13, 2020 at 10:21
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1$\begingroup$ Hi @ibio_rep1 could you please upvote the answer (ok once yuo have sufficient rep) and if you feel it resolves your question mark it as 'accepted'. This is super important because otherwise it discourages answering new OPs. $\endgroup$– M__ ♦Commented Aug 14, 2020 at 8:35
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You can also do this with pdb-tools:
pdb_selchain -A prot.pdb > prot_A.pdb
