[gmx-users] residue labeling in g_rmsf

[Tsjerk Wassenaar]

Hi Arunima,

In bash you can also combine the residue names and such with the RMSF graph:

paste <(grep "^\(ATOM\|HETATM\)" structure.pdb | cut -b 17-26 | uniq)
<(grep "^[^#@]" rmsf.xvg)

To make it a bit more clear, the redirection <( ... ) treats the output of
the command between parentheses as an input file, so we paste the results
from two commands. The first command extracts the atom residue and chain
info and uniqifies, giving a list of residues. The second command strips
the metadata fram the xvg file.

Hope it helps,

Tsjerk



On Thu, May 23, 2013 at 1:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/23/13 6:51 AM, Arunima Shilpi wrote:
>
>> Respected Sir
>>
>> If i want my residue  name to be labeled in the graph for g_rmsf ,how
>> should I proceed...
>>
>> I used the following command
>>
>> g_rmsf -f md_0_1.xtc -s md_0_1.tpr -res -o  rmsf.xvg
>>
>>
> Add labels in your favorite plotting software.  g_rmsf will not write
> residue names.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
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-- 
Tsjerk A. Wassenaar, Ph.D.