VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Tue May 10 2005 - 01:53:57 CDT

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.