[gmx-users] R: visualizing more than 9999 residues...

[Anna Marabotti]

Dear Tsjerk,
thank you very much. I really didn't know that the PDB format does not allow
more than 9999 residues (in fact, it is the first time I have such a big
system to manage). I will follow your suggestions trying to solve the
problem with chain identifiers.
Many thanks and best regards
Anna

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Message: 6
Date: Mon, 14 Feb 2011 16:43:29 +0100
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
Subject: Re: [gmx-users] visualizing more than 9999 residues....
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
	<AANLkTikVM8kt1F5p3=4O9s9kjdGVVK-PXKznRo6aNFBh at mail.gmail.com>
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Hi Anna,

The 'problem' is the PDB file format. It is a fixed-width format that
does not allow for residue numbers with more than 4 digits. Both VMD
and PyMOL do not have problems reading structures with more residues,
but they will choke if you renumber the residues, giving numbers with
five or more digits. It breaks the file format. It may be a bit
troublesome making selections if you have ambiguous residue
identifiers, but that's the way it is with PDB files. You can try to
be creative with chain identifiers and segment identifiers to give all
residues unique markers.

Cheers,

Tsjerk

On Mon, Feb 14, 2011 at 4:29 PM, Anna Marabotti
<anna.marabotti at isa.cnr.it> wrote:
> Dear gmx-users,
> I have a system formed by protein+ligand+lipid bilayer that accounts for
> about 10500 residues (56000 atoms). It seems to me that it is not possible
> to visualize correctly such a large system with Pymol or VMD, because it
> seems that the max number of residues that I can manage with both programs
> is exactly 9999. Moreover, it's not only a visualization problem, since I
> also had several problems trying to use Pymol or VMD to create the system
in
> which the protein+ligand is correctly oriented with respect to the lipid
> bilayer, to proceed further with g_membed. I had several problems in
saving
> the .pdb file (after the 9999th residue, the numbering restarted from 0;
> when I manually corrected this prroblem and re-numbered the file, I opened
> it with VMD and Python and found some aberrant visualization of the water
> molecules exceeding the number of 9999. At last, I decided to remove the
> exceeding waters).
> I know that this is a Gromacs user list, not a Pymol or VMD user list, but
> since it seems to me that these two programs are generally considered as a
> "graphical interface" with respect to Gromacs, I'd like to know how you
> folks manage this problem without removing residues. I searched for some
> hints in the gmx-user list and in Google but I didn't find anything.
> Thank you very much and sorry for this off-topic question.
> Anna Marabotti
>
> __________________________________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science - CNR
> Via Roma, 64
> 83100 Avellino
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> E-mail: amarabotti at isa.cnr.it
> Skype account: annam1972
> Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
>
> "When a man with a gun meets a man with a pen, the man with the gun is a
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>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands


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