Difference between revisions of "Rotamer Toggle"
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| − | + | ===DESCRIPTION=== | |
| + | Backbone-Dependent Rotamer library (Dunbrack, Cohen see ref) is imported into pymol giving access to this information. There are a number of different ways to use the data, I've only implemented a few as well as added extra functions that seemed useful. | ||
| + | *colorRotamers - color rotamers by closest matching rotamer angles from database; i.e. color by how common each rotamer of selection, blue - red (least to most common). | ||
| + | *Rotamer Menu - an added menu into menu.py, which displays the most common rotamers for the given(clicked) residue; you can also set the residue any of the common rotamers as well | ||
| + | *set_rotamer - routine called by above menu, but can be called manually to set a specific residues side-chain angles | ||
| + | *set_phipsi - set all phi,psi angles of given selection to given angles (useful for creating secondary structures) | ||
| − | + | To setup a rotamer menu inside the residue menu: | |
| + | *copy rotamers.py to C:/Program Files/DeLano Scientific/PyMol/modules/pymol/rotamers.py | ||
| + | *copy mymenu.py to C:/Program Files/DeLano Scientific/PyMol/modules/pymol/menu.py (WARNING : overwrites default menu.py - use at your own risk) | ||
| + | *copy bbdep02.May.sortlib to C:/Program Files/DeLano Scientific/PyMol/modules/pymol/bbdep02.May.sortlib (or newer version of sorted bbdep) | ||
| + | This is only one possible way to do this, I am sure there are many others. | ||
| + | |||
| + | ===USAGE=== | ||
| + | colorRotamers selection | ||
| + | set_rotamer selection, chi1_angle [,chi2_angle] [,chi3_angle] [,chi4_angle] | ||
| + | set_phipsi selection phi_angle, psi_angle | ||
| + | |||
| + | ===Scripts (Rotamers.py ; MyMenu.py)=== | ||
| + | <source lang="python"> | ||
| + | |||
| + | </source> | ||
| + | |||
| + | ===EXAMPLES=== | ||
| + | hide lines,all | ||
| + | hide ribbon | ||
| + | |||
| + | ===SEE ALSO=== | ||
| + | |||
| + | ===REFERENCES=== | ||
| + | Dunbrack and Cohen. Protein Science 1997 | ||
| + | |||
| + | [http://dunbrack.fccc.edu/bbdep/index.php Dunbrack Lab Page (Contains backbone-dependent library)] | ||
[[Category:Script_Library|Rotamer Toggle]] | [[Category:Script_Library|Rotamer Toggle]] | ||
Revision as of 23:59, 11 May 2005
DESCRIPTION
Backbone-Dependent Rotamer library (Dunbrack, Cohen see ref) is imported into pymol giving access to this information. There are a number of different ways to use the data, I've only implemented a few as well as added extra functions that seemed useful.
- colorRotamers - color rotamers by closest matching rotamer angles from database; i.e. color by how common each rotamer of selection, blue - red (least to most common).
- Rotamer Menu - an added menu into menu.py, which displays the most common rotamers for the given(clicked) residue; you can also set the residue any of the common rotamers as well
- set_rotamer - routine called by above menu, but can be called manually to set a specific residues side-chain angles
- set_phipsi - set all phi,psi angles of given selection to given angles (useful for creating secondary structures)
To setup a rotamer menu inside the residue menu:
- copy rotamers.py to C:/Program Files/DeLano Scientific/PyMol/modules/pymol/rotamers.py
- copy mymenu.py to C:/Program Files/DeLano Scientific/PyMol/modules/pymol/menu.py (WARNING : overwrites default menu.py - use at your own risk)
- copy bbdep02.May.sortlib to C:/Program Files/DeLano Scientific/PyMol/modules/pymol/bbdep02.May.sortlib (or newer version of sorted bbdep)
This is only one possible way to do this, I am sure there are many others.
USAGE
colorRotamers selection set_rotamer selection, chi1_angle [,chi2_angle] [,chi3_angle] [,chi4_angle] set_phipsi selection phi_angle, psi_angle
Scripts (Rotamers.py ; MyMenu.py)
EXAMPLES
hide lines,all hide ribbon
SEE ALSO
REFERENCES
Dunbrack and Cohen. Protein Science 1997