[gmx-users] Cross correlation map of residues

[Smith, Micholas D.]

If you want coloured images you can always use the xpm2ps tool. It will map the .xpm generated into a postscript file with the expected coloring.


===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Qasim Pars <qasimpars at gmail.com>
Sent: Friday, June 03, 2016 6:00 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Cross correlation map of residues

Hi,

@Tsjerk: I just installed GROMACS-3.3 and implemented g_correlation tool.
Unfortunately this tool generates the colorless correlation matrix (.xpm)
on atoms. Whereas I would like to have the colourful correlation matrix on
residues (not based on atoms). I think there is no way to get the colourful
correlation matrix on residues by g_correlation tool?

@Florent: The R package bio3d is complex :( It would be good if you share
on the user list such a code to generate the correlation matrix?

Cheers,

On 3 June 2016 at 11:27, Florent Hédin <work at fhedin.com> wrote:

> Hi,
>
> In case you really want to produce something similar, I have a solution (
> 2 in fact ;-) )
>
> This plot is easy to produce with the R package bio3d, unfortunately it
> only supports charmm/namd dcd and amber ncdf trajectory types.
>
> The first option : would be to use vmd for converting a gmx trajectory to,
> for example, dcd. Then follow the bio3d tutorials of R.
>
> The second option is : R is really modular, you can write a piece of C
> code reading the gromacs trajectory and returning it (frame by frame) to R.
> This code is compiled as a shared library, and in R you would just easily
> load it. I already have some code doing that, if interested I can share it.
> On long term I plan to put this piece of code directly into a R package.
>
> Regards,
>
> Florent Hédin
>
>
> On 03/06/16 08:02, Tsjerk Wassenaar wrote:
>
>> Hi Qasim,
>>
>> The plot you refer to is the result of NMA on C-alpha only. So g_covar
>> -xpma using only C-alpha atoms should come close. You might also want to
>> try the g_correlation tool mentioned earlier on the list, but again with a
>> selection of only C-alpha atoms.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Fri, Jun 3, 2016 at 1:50 AM, Qasim Pars <qasimpars at gmail.com> wrote:
>>
>> Dear gmx users,
>>>
>>> I need to get the cross correlation map of all residues belonging to a
>>> protein (like this figure
>>>
>>> http://thegrantlab.org/bio3d/vignettes/Bio3D_nma/figures/ex1C-dccmplot.png
>>> ).
>>> Is there any tool to get such a plot with GROMACS?
>>>
>>> By the way, gmx covar -xpma gives the cross correlation for each atom
>>> pair
>>> but it is not what I want.
>>>
>>> Any suggestions will be appreciated.
>>>
>>> --
>>> Qasim Pars
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>>
>>
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