VMD-L Mailing List

From: Ekta Khurana (ekta_at_vitae.cmm.upenn.edu)
Date: Tue May 10 2005 - 11:31:27 CDT

  Thanks Axel, The script does what I wanted!

> On Mon, 9 May 2005, Ekta Khurana wrote:
>
> hi ekta,
>
> please have a look at
>
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/mk3drama/
> or
> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part6.html#chap8_sect5
> for a more detailed description of the script.
>
> EK> Thanks for the reply.I am doing this but I want the points for
> all
> EK> the residues in one plot. I can get this for one individual frame but
> not all.
> EK> Ekta
>
> since this is using vmd scripting to accumulate the data,
> you can have it any way you want, i.e. all of the protein, or
> just part of it for all of the trajectory or in part.
>
> the only drawback of that script is that it is (not yet) creating
> a smooth surface. it you have enough data, it should not matter
> so much. for that i also have some code to convert those kind of
> histograms to data sets readable with OpenDX (http://www.opendx.org/),
> which is much more powerful for visualization of that kind of data,
> but also a bit more complicated to learn.
>
> best regards,
> axel.
>
> EK>
> EK> On Mon, 9 May 2005, Michel Espinoza-Fonseca wrote:
> EK>
> EK> > According to what I know, after reading your trajectory file, you
> can
> EK> > automatically get the Ramachandran plot for the entire simulation.
> The
> EK> > only thing you need to do is to open both topology and trajectory
> files,
> EK> > go to Extensions-->Analysis-->Ramachandran plot. Then you pick the
> EK> > residue you're interested in and you'll get a bunch of points, each
> one
> EK> > representing the phi/psi angles.
> EK> >
> EK> > Peace,
> EK> > Michel
> EK> >
> EK> > -----Original Message-----
> EK> > From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On
> Behalf
> EK> > Of Ekta Khurana
> EK> > Sent: Monday, May 09, 2005 6:08 PM
> EK> > To: vmd-l_at_ks.uiuc.edu
> EK> > Subject: vmd-l: Rama plot
> EK> >
> EK> >
> EK> > Hi, Is there a way I can plot the phis and psis of the residues for
> EK> > all
> EK> > the frames instead of moving frame by frame using Rama plot in the
> pull
> EK> > down menu to get a complete picture of which areas of the
> Ramachandran
> EK> > plot are most densely populated.
> EK> > Thanks,
> EK> > Ekta
> EK> > --
> EK> >
> EK> >
> EK> >
> EK> >
> EK>
> EK>
>
> --
>
> =======================================================================
> Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
> Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
> Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
> D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
> 

-- 
Ekta Khurana
Center for Molecular Modeling
University of Pennsylvania
email:ekta_at_cmm.upenn.edu
      ekhurana_at_sas.upenn.edu
Phone: (215) 573-8697
Fax: (215) 573-6233