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
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. 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. 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: [email protected]
