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MSL-Libraries

MSL: an open source C library for analysis, manipulation, modeling and design of macromolecules. MSL: an open source C library for analysis, manipulation, modeling and design of macromolecules. Is a open source C software library for molecular modeling produced in the Senes Lab. At the University of Wisconsin-Madison, in collaboration with a team or researchers from a number of Universities and companies. The MSL library is not. Some of the features supported by the library are:. Structure building from ...

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MSL: an open source C library for analysis, manipulation, modeling and design of macromolecules. MSL: an open source C library for analysis, manipulation, modeling and design of macromolecules. Is a open source C software library for molecular modeling produced in the Senes Lab. At the University of Wisconsin-Madison, in collaboration with a team or researchers from a number of Universities and companies. The MSL library is not. Some of the features supported by the library are:. Structure building from ...

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https://msl-libraries.org

MSL: an open source C library for analysis, manipulation, modeling and design of macromolecules. MSL: an open source C library for analysis, manipulation, modeling and design of macromolecules. Is a open source C software library for molecular modeling produced in the Senes Lab. At the University of Wisconsin-Madison, in collaboration with a team or researchers from a number of Universities and companies. The MSL library is not. Some of the features supported by the library are:. Structure building from ...

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msl-libraries.org

1

MSL Objects - MSL-Libraries

http://www.msl-libraries.org/index.php/MSL_Objects

MSL contains two object for representing a macromolecule: the AtomContainer. Is a simple, light containers for the molecules represented internally just as an array of Atom. Is a structured, hierarchical representation of the molecules, more complex, powerful object than the AtomContiner, supports energy calculations. It contains Chain. Objects and a whole hierarchy all the way to the Atom. A polypeptide chain. Takes a letter as an identifier ("A", "B") as in a PDB file. It contains Position.

2

Special pages - MSL-Libraries

http://www.msl-libraries.org/index.php/Special:SpecialPages

Pages with the fewest revisions. Pages without language links. All pages with prefix. Pages with a page property. Login / create account. Recent changes and logs. Gallery of new files. Media reports and uploads. List of files with duplicates. Search for duplicate files. Random page in category. Redirect by file, user, page or revision ID. Pages with the most categories. Pages with the most interwikis. Pages with the most revisions.

3

Tutorial:Getting started: Downloading MSL - MSL-Libraries

http://www.msl-libraries.org/index.php/Tutorial:Getting_started:_Downloading_MSL

Tutorial:Getting started: Downloading MSL. Is open source software distributed under the terms of the GNU Lesser General Public. MSL is available from SourceForge, at the project page. Stable releases) and at the SVN repository. Stable, betas, development version). Version 1.1, released 3 April, 2013. Version 1.0,released 8 July, 2013. V11, stable release, created Apr 3, 2013, last update (v.1.1.0.9) Feb 11, 2014. Svn checkout svn:/ svn.code.sf.net/p/mslib/code/trunk mslib/trunk. Svn ls -v /tags. Added a...

4

ToDo - MSL-Libraries

http://www.msl-libraries.org/index.php/ToDo

Add support for wild cards in CHARMM parameter file (used in param 19, not used in 22). Documentation at http:/ www.charmm.org/html/documentation/c32b2/miscom.html. Implement: 1) copy constructor; 2) void deleteInteractionsWithAtom(Atom and a); 3) void deleteInteractionsWithAtoms(AtomPointerVector and atomVec);. Implement removeIdentity and mutate functions. Create PDBToplogy object for adding residues to positions. Copy bonds in copy costructor. Proper support for MODELs and alt coordinates.

5

PyMOL Python Interface - MSL-Libraries

http://www.msl-libraries.org/index.php/PyMOL_Python_Interface

Install PyMOL by going here: http:/ www.pymol.org/. First you need to make the PythonMSL.so library ( Pre-compiled libraries should be available in the future ). Make all objects via make. Depending if you are on linux or mac). On a Mac you need to ln -s MSLDIR/PythonMSL.so /Applications/PyMOLX11Hybrid.app/pymol/modules/PythonMSL.so. Copy MSLDIR/exampleFiles/pymolrc.py to USERNAME/.pymolrc.py. After loading a PDB file, in the PyMOL window, type getSasa("all").

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seneslab.org

The Senes Lab, Department of Biochemistry, University of Wisconsin-Madison

http://www.seneslab.org/software.html

MSL (Molecular Software Libraries). MSL is an open source C library for analysis, manipulation, modeling and design of macromolecules. For download and documentation go to the MSL project wiki. 433 Backcock Dr., Room 419. Madison, WI 53706. Office ( 1) 608-890-2584. Lab ( 1) 608-262-7355.

seneslab.org

The Senes Lab, Department of Biochemistry, University of Wisconsin-Madison

http://www.seneslab.org/publications.html

Armstrong CR, Senes A. Screening for transmembrane association in divisome proteins using TOXGREEN, a high-throughput variant of the TOXCAT assay". Biochim. Biophys. Acta. Barth P, Senes A. Toward high-resolution computational design of the structure and function of helical membrane proteins". Nat Struct Mol Biol. The computational design of α-helical membrane proteins is still in its infancy but has already made great progress. De novo design allows stable, specific and active minimal oligomer...Store d...

senes.biochem.wisc.edu

The Senes Lab, Department of Biochemistry, University of Wisconsin-Madison

http://senes.biochem.wisc.edu/software.html

MSL (Molecular Software Libraries). MSL is an open source C library for analysis, manipulation, modeling and design of macromolecules. For download and documentation go to the MSL project wiki. 433 Backcock Dr., Room 419. Madison, WI 53706. Office ( 1) 608-890-2584. Lab ( 1) 608-262-7355.

senes.biochem.wisc.edu

The Senes Lab, Department of Biochemistry, University of Wisconsin-Madison

http://senes.biochem.wisc.edu/publications.html

Armstrong CR, Senes A. Screening for transmembrane association in divisome proteins using TOXGREEN, a high-throughput variant of the TOXCAT assay". Biochim. Biophys. Acta. Barth P, Senes A. Toward high-resolution computational design of the structure and function of helical membrane proteins". Nat Struct Mol Biol. The computational design of α-helical membrane proteins is still in its infancy but has already made great progress. De novo design allows stable, specific and active minimal oligomer...Store d...

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MSL: an open source C library for analysis, manipulation, modeling and design of macromolecules. MSL: an open source C library for analysis, manipulation, modeling and design of macromolecules. Is a open source C software library for molecular modeling produced in the Senes Lab. At the University of Wisconsin-Madison, in collaboration with a team or researchers from a number of Universities and companies. The MSL library is not. Some of the features supported by the library are:. Structure building from ...

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