Re: Re: vmd-l: rmsd matrix

From: Luis Gracia (lgraval_at_gmail.com)
Date: Thu Sep 03 2009 - 16:47:36 CDT

Hi, you could also use the rmsdtt plugin and activate the 'All' option in
the trajectory section. Then save the results to file. You will get 5
columns specifiying the molecule/frame pairs and the resulting rmsd.
Converting this file to a matrix like should be trivial.

Another option is to use the
itrajcomp<http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/itrajcomp/>plugin
which will create an interactive matrix for you, which can be saved
to file in different formats, matrix-like included. With this plugin you can
do other types of calculations, like covariance, distance, angles, radius of
gyr, ... or create your custom calculations. The selection of atoms is very
flexible and allows to automatically do the calculation over any number of
frames and molecules.

Contact me if you are interested in itrajcomp.

Best

Luis

Luis Gracia, PhD
Scientific Software Specialist
Department of Physiology & Biophysics
Weill Cornell Medical College
1300 York Avenue, Rm LC-501F
New York, NY 10065

Tel: (212) 746-6375
Fax: (212) 746-6226
lug2002_at_med.cornell.edu

On Thu, Sep 3, 2009 at 12:23 PM, Cesar Millan <pachequin_at_gmail.com> wrote:

> Hi andres, I'll recommend you to use Simulaid (free for academics) that is
> develop by Prof. Mihaly Mezei. (
> http://atlas.physbio.mssm.edu/~mezei/simulaid/>).
> Simulaid can do the analysis that you want in a simple manner.
>
> Best regards.
>
> On Thu, Sep 3, 2009 at 7:45 AM, Andres Morales N <
>
andresmoralesn2_at_hotmail.com> wrote:
>
>>
>>
>> Dear VMD users:
>>
>> I was using script below to calculte a matrix that contains rmsd between
>> structures from a dcd file:
>>
>> set outfile [open rmsd_min.txt w];
>> set sel1 [atomselect top "protein and backbone and noh"]
>> set nf1 [molinfo top get numframes]
>> set sel2 [atomselect top "protein and backbone and noh"]
>>
>> for {set i 0 } {$i < $nf1 } { incr i } {
>> for {set j $i } {$j < $nf1 } { incr j } {
>>
>> $sel1 frame $i
>> $sel2 frame $j
>>
>> $sel2 move [measure fit $sel2 $sel1]
>> set rmsd_matrix($i,$j) [measure rmsd $sel2 $sel1]
>> $sel2 move [measure fit $sel2 $sel1]
>> set rmsd_matrix($j,$i) [measure rmsd $sel2 $sel1]
>> }}
>>
>> for { set i 0 } { $i < $nf1 } { incr i} {
>> for { set j 0 } { $j < $nf1 } { incr j } {
>> puts -nonewline $outfile "$rmsd_matrix($j,$i) "
>> }
>> puts $outfile ""
>> }
>> close $outfile
>>
>> It was working well. I created a mutated structure and now I need to
>> calculate RMSD matrix between structures from both dcd files (one of native
>> structure and another from mutated structure), and I do not know how
>> I should change the script above to do it. I wait somebody can help me.
>>
>> Thanks for your suggestions
>>
>> King regards
>>
>> Andres
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
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>
>
>
> --
> ############################
> César Millán Pacheco
> Facultad de Ciencias
> Universidad Autonoma del Estado de Morelos
> Tel: 777 3297020
> Fax: 777 3207040
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> pachequin_at_gmail.com
>

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