DivScore: A Plugin for PyMOL
The DivScore package is intended to be used with AMBER
and
DivCon
for preprocessing biological structures (primarily proteins and small molecules)
quick geometry optimization, charge calculation, creating job scripts and
streamlining workflow within the PyMOL
environment. This package was developed to aid my research
and hence works within the confines of assumptions that were necessary
for streamlining my workflow. However for those who have access to the
AMBER and DivCon, it could potentially be useful since it combines the
power of PyMOL with that of AMBER for molecular simulation and DivCon for
Quantum Mechanics calculations on large biomolecular systems. An example
of the capability of DivScore is that, it can perform a quick minimization
of a ligand in the active site of a protein based on the AMBER force field
and upload the resulting coordinates into PyMOL for visualization. More
examples of things one could do will follow in the examples sections.
1.) Protonate proteins and small molecules*
2.) Minimize small molecules/Ligands/Drugs*
3.) Minimize proteins, ligands in complexes*
4.) Calculate charges on small molecules**
5.) Alter Residue description in the Proteins
6.) Setup DivCon Input Files
7.) Setup job scripts for doing Energy Minimization,
MD simulation, and QM DivCon runs.
8.) Other features:
1. load multiple files according to a pattern [Usage: mload inh*.pdb]9.) DivScore enables PyMOL to recognize the following UNIX commands:
2. get charge on a fragment of a protein [Usage: fchg OBJECT]
3. calculate surface area of a fragment of a molecule [Usage: sasa OBJECT]
4. calculate surface area burial in complexation [Usage: dasa OBJECT]
5. display sequence of a protein or a fragment [Usage: gsq OBJECT]
1. cp [Usage: cp path/file1 path/file2]* Needs AMBER; ** Needs DivCon
2. cat [Usage: cat path/filename]
3. head [Usage: head path/filename]
4. rm [Usage: rm path/filename]
5. mkdir [Usage: mkdir directory name]
6. shc [Usage: shc "any shell command" use with caution]
7. mv [Usage: mv path/file1 path/file2]
1) copy the
file ramm.tar.gz to your pymol distribution home (PYMOL_HOME) as:
% cp ramm.tar.gz $PYMOL_HOME/pymol/modules/pmg_tk/startup/
2) gunzip
and untar the distribution:
% tar xzvf ramm.tar.gz OR gunzip ramm.tar.gz ; tar xvf ramm.tar
You will see a directory ramm that will be created.
Then launch PyMOL. DivScore will ask you a few questions to initialize
its path. You have to provide the path for your AMBER distribution and
DivCon distribution. DivScore will store the initialization information
for future use. Now you are good to go. In case of an unsuccessful installation
feel free to contact me
o For protonating small molecules BABEL is needed. Open source babel version can be obtained from OpenEye. Here is a compiled copy for RH7. For protonate feature of DivScore plugin to function babel should reside in the $HOME/bin/ directory.
o For disulfide linking the program Disulphide (written by Andrew Wollacott) is needed. For
crosslinking feature of DivScore plugin to function Disulphide should
reside in the $HOME/bin/ directory.
o For small molecules the program rename is needed and can be downloaded
for RH7 from here.
This program should reside in the $HOME/bin/ directory.
o An older version of PyMOL for which this plugin was originally created can
also be found here.