[gmx-users] Secondary structure not visible after convertingfrom .gro to .pdb

[Christopher Neale]

I sometimes see this in VMD if the coordinates are truly awful (e.g, if the C-alpha atoms are way too far apart, then VMD does not recognize it as a proper backbone since no topology information is loaded and connectivity is inferred from distances). I also see this for some crystal structures (in VMD) and I am not sure exactly why, but I presume that something is not falling into an "accepted" region of conformational space to be recognized as a protein backbone. I presume the same is true for Pymol.

Try to run a very small amount of MD and see if that improves things. It always does for me.

Chris.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of bharat gupta <bharat.85.monu at gmail.com>
Sent: 28 May 2014 21:36
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Secondary structure not visible after convertingfrom .gro to .pdb

I am not concerned about secondary structure changes. But I want to
visualize the entire protein structure in ribbon form after energy
minimization... When I see the converted structure (.gro to .pdb) in pymol,
only one chain is visible. How can I see all the chains together


On Thu, May 29, 2014 at 10:28 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

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> On 5/28/14, 9:24 PM, bharat gupta wrote:
>
>> Hi,
>>
>> I energy minimized a protein consisting 10 chains using gromacs. When I
>> converted the structure of the protein from gro format to pdb format to
>> visualize in Pymol, it shows only one chain in ribbon form and rest of the
>> chains are not shown ... How to rectify this error ??
>>
>>
> Visualization programs guess what secondary structure should be based on
> the supplied geometry.  Sometimes they get it wrong.  If you're concerned
> about secondary structure changes, you should be using a quantitative
> method rather than visualization.
>
> -Justin
>
> --
> ==================================================
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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--
Bharat
Ph.D. Candidate
Biomolecular Engineering Laboratory
Pusan National University
South Korea
Mobile no. - 010-5108-3680
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