Revision as of 11:58, 31 January 2013

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 is a PyMOL wizard for in silico spin labeling of proteins.

News

2013-01-31:

Version 1.1 uploaded - should be available soon.

Some new features:

Much faster. The algorithm was optimized and the speed of the program is now almost independent on the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.

New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.

Distances and histogram are directly copied to the clipboard or written out to a file as before.

Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also,only the average and c-Beta distances are displayed in the PyMOL viewer to make it easier to read of the values.

The new version was thoroughly tested. I case of problems, please use the contact address below.

Version 1.0 will still be available in the repository.

Program features

Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported.

Please reference:

MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL, Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0

Screen shot

Usage

Installation

Install the program by copying the code from the link above 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. Alternatively install the wizard via the plugins menu.

mtsslWizard has been tested with PyMOL 1.5.

Additional requirements:

SciPy has to be installed for v1.1
On some systems pyperclip or xerox have to be installed for the clipboard support.

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 "Speed" and "vdW restraints". Speed determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.
click "Search conformers" to start the calculation.

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

@@ Line 51: / Line 51: @@
 #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.
+#If needed, vary the search parameters like "Speed" and "vdW restraints". Speed determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.
-#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.
+#click "Search conformers" to start the calculation.
 ===Distance calculation===
 #change "Mode" to "Distance"

MtsslWizard: Difference between revisions