Hi Thomas,
Probably something like this should do something close to what you need:
sed -n '/^\(ATOM\|HETATM\)/s/^.\{16\}\(.\{10\}\)/\1 \0/p' file.pdb | sort
-n -k 3 | cut -b 11-
Hope it helps,
Tsjerk
On Thu, May 30, 2013 at 10:21 AM, Thomas Evangelidis <teva...@gmail.com>wrote:
> Dear PyMOL users/developers,
>
> Is there any way to rearrange the atom records in a .pdb file according to
> their residue ID? I have run Vina with flexible sidechains and then
> concatenated the rigid receptor part with the sidechain conformations for
> each pose. That resulted to .pdb files where the backbone atoms (apart from
> Ca) occur in the correct order but the flexible sidechain atoms are at the
> end of the file. That leads to some problems in visualization and analysis
> of the protein-ligand complexes that I'd like to overcome. If anyone know
> how to fix that problem either with PyMOL or any other program please let
> me know.
>
> thanks,
> Thomas
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tev...@pharm.uoa.gr
>
> teva...@gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
>
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--
Tsjerk A. Wassenaar, Ph.D.
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