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MtsslWizard
| Type | PyMOL Plugin |
|---|---|
| Download | plugins/mtsslWizard.py |
| Author(s) | Gregor Hagelueken |
| License | - |
| This code has been put under version control in the project Pymol-script-repo | |
mtsslWizard
mtsslWizard is a PyMOL wizard for in silico spin labeling of proteins.
News
2013-01-17:
We are just working on Version 1.1 of mtsslWizard. It will come out end of January 2013.
Some new features:
- much faster
- new spin labels
- distances and histogram are directly copied to your clipboard
- improved interface
If you are interested in a test version, please contact hagelueken'at'pc.uni-bonn.de
Program features
An MTSSL spin label can be attached to any position of a protein just by pointing and clicking. The program can then search the conformational space of the label (5 chi angles) and determine which conformations of the label do not clash with the protein surface. In "distance mode", distances between MTSSL ensembles can be determined and exported. For symmetric molecules, the MTSSL ensemble can be copied to symmetry related positions simply by pointing and clicking ("Copy & Move" mode).
Please reference:
Screen shot
Usage
Installation
Install the program by copying the code below into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. mtsslWizard has been tested with PyMOL 1.4.
Labeling
- Open a protein structure in PyMOL and remove any unwanted solvent molecules or ligands.
- Start the mtsslWizard via Wizards>mtsslWizard
- If needed, vary the search parameters like "Thoroughness", "Cutoff" and "Clashes allowed". Thoroughness determines how many conformations of MTSSL will be checked. The cutoff value determines the minimum allowed distance between label and protein before the conformation is sorted out as clashing. "Clashes allowed" should usually be set to zero. If this value is changed to e.g. "5", a conformation can violate the "cutoff" parameter five times before the conformation is discarded.
- click "Go" to start the calculation. Depending on the size of the protein, the "Thoroughness" parameter and of course the speed of your computer the duration of the search can vary quite considerably. With the default settings it does usually not take longer than 10-15 seconds.
Distance calculation
- change "Mode" to "Distance"
- click the first and second ensemble
- The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take quite a while!
Reference
If you find this program useful, please cite this paper:
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.
Contact
hagelueken'at'pc.uni-bonn.de