[PyMOL] Generating Protien Motions with ANM web server and PyMOL

[Yang, Z. <pro...@gm...>]

Dear PyMOL users:

A web server of ANM (Anisotropic network model) has been recently =
developed
in our group. ANM is a coarse-grained normal mode analysis (NMA) tool =
for
analyzing the equilibrium dynamics of proteins introduced in 2000 by =
Bahar
and coworkers [1, 2]. The ANM web server has been recently constructed =
[3],
and is being presently maintained, by Dr. Eran Eyal.
http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi=20

I wrote a code to read in the output files from the web server and to
generate a series of PyMOL script files. This code can be executed from =
the
web site, so that the user can easily download these files and display =
the
motions of proteins using PyMOL for any input PDB files.

In order to generate the PyMOL scripts:

1) Fill in the PDB ID at the server main page,
http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi   Other input options =
may
also be changed, such as defining a model number for NMR structure, or
biological unit to x-ray crystallography file.

2) Wait for a few seconds for the calculation, and then you will be
redirected to the results page, with Jmol viewer on the top.

3) On the bottom of that page, there is a link, titled 'Create PyMol
script'. Click on it, to open another setting page.

4) In the page of 'Create PyMol scripts to visualize vibrations', =
complete
the
movie settings and submit them.

5) Finally, a downloading page will appear. You can choose download =
either
an overall zip file or separated files for each mode.

6) Unzip the downloaded files to one folder and run the *.pml files.=A0

Comments:

1) This web server can generate the essential (slowest) 20 modes of =
motion.
If you need more than 20 modes, contact us directly.

2) The arrows files are written with PyMOL CGO, so you can use =
ray-tracing.

3) To show the cartoon view, make sure your PDB files have the secondary
structure information.

4) The structures are colored by the mobilities of the individual =
residues
in the selected vibrational mode.=A0=A0

5) You can change the motion speed (i.e. frequency of fluctuations) in
PyMOL, top toolbar 'Movie->Speed->*FPS'

6) You can use the command, 'mpng' to get a series of png figures, for
further work.

Last but not least, for any question and suggestion, please feel free to
contact us! Your feedback is our motivation of improvement.


References:

1. . Doruker, P, Atilgan, AR & Bahar, I. (2000). Dynamics of proteins
predicted by molecular dynamics simulations and analytical approaches:
application to a-amylase inhibitor. Proteins 40, 512-524.

2. Atilgan, AR, Durrell, SR, Jernigan, RL, Demirel, MC, Keskin, O. & =
Bahar,
I. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic
network model" Biophys. J. 80, 505-515.

3. Eyal E, Yang LW, Bahar I. (2006) Anisotropic Network Model: =
systematic
evaluation and a new web interface. Bioinformatics, in press.



Zheng Yang

Department of Computational Biology
University of Pittsburgh
3064 BST3, 3501 Fifth Avenue
Pittsburgh, PA, 15260
Fax: 412-648-3163
Email: pro...@gm...