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

[Justin Lemkul]

On 5/28/14, 9:36 PM, bharat gupta wrote:
> 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
>

Consult the PyMOL documentation; this is not a Gromacs issue.

-Justin

>
> 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
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
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>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================