Editing MtsslDock (section)

==Docking==
To do a docking run, label the two proteins with [[MtsslWizard | mtsslWizard (1.1)]] and then start mtsslDock from the Plugins menu. 
The GUI should then appear and look like this:

[[File:MtsslDock Import Labels.jpg | 500px]]

First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".

The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":

[[File:MtsslDock distanceTable.jpg | 500px]]

You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.

Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.
Once the docking has finished, a "Results" tab will be added to the GUI:

[[File:MtsslDock results.jpg | 500px]]

Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.

===C2 symmetric structures, e.g. symmetric dimers===
If you try the C2 dimer feature: Make a copy of your monomer and leave it at the exact same position. Then, label both monomers independently and import them as protein A and B.

The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.