The ViewMatch Plugin
Whether you use the online server or the command line version of LabelHash, you will probably want to visually inspect your matches. We have developed a plugin for Chimera called ViewMatch that allows you to do just that. Below you will find detailed instructions on installing and using this plugin.
Installation instructions for ViewMatch
- Download and uncompress the ViewMatch plugin
- You need a local copy of the Protein Data Bank (or at least the PDB files in your match files). You can download a copy of the PDB that is used on the web server. It is a huge 8.0GB download. Instead, you can also create your own mirror of the PDB. See the instructions at the PDB on creating a mirror of the PDB. Open ViewMatch/Match.py in an editor and change the PDBPATH variable, so that it includes the directories where you have stored your PDB files. If you have the entire PDB, something like this should work:
PDBPATH = [ '/path/to/PDB/data/structures/all/pdb' ]
On Windows use backward slashes ('\') instead of forward slashes ('/') as directory separators. - Download and install a recent version of Chimera. ViewMatch relies on the python2.5 ElementTree module for XML parsing. Recent versions of Chimera already contain this module, but older versions of Chimera are bundled with python2.4, which does not contain this module. If your machine does not have python2.5 installed, install that first. One can then simply create a symbolic link to the python2.5 xml directory like so:
ln -s /usr/lib/python2.5/xml ~/labelhash/ViewMatch/xml
Recent versions of Chimera are using python2.5. So if you are using a recent version, then the step above is unnecessary. - Start Chimera. Go to the Favorites menu and select Preferences. Select the Tools category in the top left of the Preferences window. Click the Add button and select the directory that contains the ViewMatch directory (not the ViewMatch directory itself). If you plan to use the ViewMatch plugin often, you may wish to add ViewMatch to the Toolbar and your Favorites as shown below. Restart Chimera.
Using the ViewMatch plugin
The ViewMatch plugin is derived from the ViewDock plugin that comes with Chimera. To load an XML file with matches, go to the Tools menu, select the Structure Comparison submenu, and select ViewMatch. If you have added ViewMatch to the toolbar you can just click on the ViewMatch icon. In the file dialog window that comes up select your file with matches. ViewMatch will read the first 100 matches in the file. It gets the atom coordinates for the matches from PDB files. After loading is finished, the main Chimera window will show the motif in transparent white superimposed with a match:
The ViewMatch controller window should look something like this:
The name of a match is its PDB ID followed by the chain ID. For each match we show the RMSD to the motif, the p-value, the depth, and the score. The depth is the average distance of the match residues to the molecular surface. The score is the number of matching residues. In the web version of LabelHash only complete matches are computed, so this number will be the same for all matches.
The bottom half of the window shows additional information for the currently selected match. This includes the EC class and Gene Ontology (GO) annotations, if known. The PDB-to-EC mapping comes from PDBSProtEC site. The GO terms are taken from the Jena Library. Also included are the REMARK records from the PDB files. Finally, the matching parameters are added. The matching parameters are the same for all matches.
For each match only the matching residues are shown. By pressing the "Load PDB file" button, the entire PDB file is loaded for the selected match and aligned with the motif. By default it shown in the ribbon representation. If more information about certain matches is needed, press the PDBsum button. This will open the corresponding PDBsum web pages in your browser for the selected matches.