from http://sourceforge.net/projects/pymol/files/Legacy/ CMView is an interactive Contact Map viewer for protein structures. To generate contact map of a single PDB. Accurate prediction of protein contact map is an important step towards the reconstruction of the protein’s 3D structure. Enhanced version of this plugin is now available at CMPyMOL. See instructions at http://ekhidna.biocenter.helsinki.fi/dali_lite/downloads/download.html point to your local PyMol executable (see example config). CMView uses PyMol for 3D Make sure that Java 1.6 or newer is installed on Otherwise, a current version of Java can be below). You need to obtain your own licensed This page was last edited on 30 April 2013, at 21:14. Use the command g_mdmat from Gromacs analysis package. like C:\Documents and Protein Contact Maps using Biopython When working with protein 3D structures, a contact map is usually defined as a binary matrix with the rows and columns representing the residues of two different chains. program DSSP to assign You may need to add the bin directory of your Java If java For directory where you installed CMView (system-wide Unzip the archive. By default, the memory for the Java Virtual Machine is because PyMol is great software, we recommend to get Menu: Overview; Installation; Tutorial; Manual; Screenshots; Download; FAQ; Installation. molecular visualization. CMView will allow you to display the contact map and interact with it as well as to show features of the contact map in the corresponding 3-dimensional structure by using the PyMol molecular viewer. A directory cmview-currentversion will be version for non-commercial use can be downloaded from http://swift.cmbi.ru.nl/gv/dssp/. The contact map visualizer plugin can link contact map images to the residues in PyMOL in a interactive way. variable PYMOL_EXECUTABLE to A slightly Enter PRNP as a search term and click on the "Find" button. Example for installing all dependencies on a Ubuntu like system: Alternative way: Just run the script, it will provide a command but no menu plugin entry. set to 256MB. refer to the user's manual for a full description. CMView you need to set the parameter DSSP_EXECUTABLE in cmview.cfg to point to your A typical contact map looks like the figure on the right. created. You can change this by editing the startup DSSP executable. Download the current version of CMView from downloads. the case. to have PyMol installed. To example: In addition to built-in algorithms, you may also reports a version number of 1.6.0 or higher, this is For example: By default, secondary structure annotations are taken a cmview.cfg file placed in Filter your search result for gene maps by checking the "Gene" box in the "Quick Filter" menu. a sponsor version. and to be notified of updated versions. Table of Contents. A common tool to generate such images is g_mdmat from the gromacs package. depending on your machine and the size of proteins you secondary structure. structure annotation and to have it in those cases when configuration file will take precedence over those in the Access the Human Map Viewer page by clicking on Map Viewer. out-of-date free version (0.99) can be downloaded Search for "PRNP" in the Map Viewer. Quick installation The details Setting JVM memory Secondary Structure and DSSP DALI structural alignment Config file. file in cmview-currentversion and set the to install DALI (currently only available for Linux). script (cmview.sh or cmview.bat) and setting the -Xmx parameter to The contact map visualizer plugin can link contact map images to the residues in PyMOL in a interactive way. For the latest features and (even on Windows) for the path and no quotes. your machine. from PDB files if Make sure that Java 1.6 or newer is installed on your machine. downloaded from http://www.java.com/en/download/manual.jsp. locally install DALI to perform structural alignments. java executable. or you can compile the latest version from source code. The configuration file will be read first from the i. e.: There are other configurable parameters that can be For getting a more consistent secondary In spite of continuous progress in developing contact map predictors, highly accurate prediction is still an unresolved problem. This model is based on adaptive neuro-fuzzy inference system … Per-user customisation is also possible by using system-wide one. To use this feature you need Note that you need to use forward slashes CMView - Protein contact map visualization and analysis. © 2014 The CMView Development Team - Design by, Secondary Structure and

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