From: Anasuya D. <an...@mb...> - 2013-04-04 10:25:50
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Hello, I wanted to know if its possible in PyMOL to split a PDB file with multiple chains,into its component chains and make smaller PDB files corresponding to each chain. For eg: I have a pdb file, 1a55.pdb, having chains P,Q and R. How do I make split it to separate components like 1a55_P.pdb, 1a55_Q.pdb, 1a55_R.pdb Also, in case I have a large number of multiple chain PDB files, how could I go about splitting each of them? Please help. - Anasuya Dighe -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. |
From: Andreas F. <doc...@gm...> - 2013-04-04 10:43:27
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Hi Anasuya, load 1a55.pdb create 1a55_P, 1a55 and c. P create 1a55_Q, 1a55 and c. Q create 1a55_R, 1a55 and c. R save 1a55_P.pdb, 1a55_P save 1a55_Q.pdb, 1a55_Q save 1a55_R.pdb, 1a55_R Andreas On 04/04/2013 11:19, Anasuya Dighe wrote: > Hello, > > I wanted to know if its possible in PyMOL to split a PDB file with multiple > chains,into its component chains and make smaller PDB files corresponding to > each chain. > > For eg: I have a pdb file, 1a55.pdb, having chains P,Q and R. How do I make > split it to separate components like 1a55_P.pdb, 1a55_Q.pdb, 1a55_R.pdb > > Also, in case I have a large number of multiple chain PDB files, how could I go > about splitting each of them? > > Please help. > > - Anasuya Dighe > > -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk |
From: Tsjerk W. <ts...@gm...> - 2013-04-04 10:51:27
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Hi Anasuya, You can make the selections in PyMOL and save each chain separately. But if you have to do batch processing, you're probably better off using sed: sed -n "/^.\{21\}P/p" 1a55.pdb > 1a55_P.pdb sed -n "/^.\{21\}Q/p" 1a55.pdb > 1a55_Q.pdb sed -n "/^.\{21\}R/p" 1a55.pdb > 1a55_R.pdb To automate completely, you can do (in bash): pdb=1a55.pdb for chain in $(grep "^ATOM" $pdb | cut -b 22 | sort -u); do sed -n "/^.\{21\}$chain/p" $pdb > ${pdb%.pdb}_$chain.pdb; done You can make that a small script, like 'chains.sh', containing: #!/bin/bash pdb=$1 for chain in $(grep "^ATOM" $pdb | cut -b 22 | sort -u) do sed -n "/^.\{21\}$chain/p" $pdb > ${pdb%.pdb}_$chain.pdb done That script you can run giving a pdb file as argument. Hope it helps, Tsjerk On Thu, Apr 4, 2013 at 12:19 PM, Anasuya Dighe <an...@mb...>wrote: > Hello, > > I wanted to know if its possible in PyMOL to split a PDB file with multiple > chains,into its component chains and make smaller PDB files corresponding > to > each chain. > > For eg: I have a pdb file, 1a55.pdb, having chains P,Q and R. How do I make > split it to separate components like 1a55_P.pdb, 1a55_Q.pdb, 1a55_R.pdb > > Also, in case I have a large number of multiple chain PDB files, how could > I go > about splitting each of them? > > Please help. > > - Anasuya Dighe > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > > > ------------------------------------------------------------------------------ > Minimize network downtime and maximize team effectiveness. > Reduce network management and security costs.Learn how to hire > the most talented Cisco Certified professionals. Visit the > Employer Resources Portal > http://www.cisco.com/web/learning/employer_resources/index.html > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Tsjerk A. Wassenaar, Ph.D. |
From: Robert C. <rob...@qu...> - 2013-04-04 13:29:16
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Hello Anasuya, On Thu, 2013-04-04 15:49 EDT, Anasuya Dighe <an...@mb...> wrote: > Hello, > > I wanted to know if its possible in PyMOL to split a PDB file with > multiple chains,into its component chains and make smaller PDB files > corresponding to each chain. > > For eg: I have a pdb file, 1a55.pdb, having chains P,Q and R. How do I > make split it to separate components like 1a55_P.pdb, 1a55_Q.pdb, > 1a55_R.pdb > > Also, in case I have a large number of multiple chain PDB files, how > could I go about splitting each of them? In addition to the other (manual) answers, there is a script on the PyMOL wiki that does exactly this. See: http://www.pymolwiki.org/index.php/Split_chains Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc |