[gmx-users] Atom names mismatch - PyMol retain order

[Erik Marklund]

Martin Höfling skrev:
> Am Freitag, 30. Mai 2008 schrieb George Abadir:
>
>   
>> atoms. Then in the simulation I used the initial PDB file generated by
>> PYMOL. Does this make things any more reasonable. Because actually, this
>> happened in five different simulations till now!!!! So, I don't think it
>>     
>
> Just as a side comment on using PYMOL: If one wants to preserve ordering of 
> atoms on loading and thus exporting one can set this (e.g. in the .pymolrc).
>
> This is what I use for editing molecules generated with pdb2gmx.
> ...
> set retain_order,1
> set pdb_retain_ids,1
> ...
>
> Best
> 	Martin
>   
Now that is one extremely good tip! I shall remember that.

/Erik

-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
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erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys