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 <anas...@mbu.iisc.ernet.in>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
>
>
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--
Tsjerk A. Wassenaar, Ph.D.
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