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

[bharat gupta]

okay ,... thanks


On Thu, May 29, 2014 at 10:38 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>>
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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
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