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In progress... checking/fixing a few minor details to make things more robust... I'll post it later tonight
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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).
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*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
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*set_rotamer - routine called by above menu, but can be called manually to set a specific residues side-chain angles
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*set_phipsi - set all phi,psi angles of given selection to given angles (useful for creating secondary structures)
  
Dan Kulp
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To setup a rotamer menu inside the residue menu:
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*copy rotamers.py to C:/Program Files/DeLano Scientific/PyMol/modules/pymol/rotamers.py
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*copy mymenu.py  to C:/Program Files/DeLano Scientific/PyMol/modules/pymol/menu.py (WARNING : overwrites default menu.py - use at your own risk)
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*copy bbdep02.May.sortlib to C:/Program Files/DeLano Scientific/PyMol/modules/pymol/bbdep02.May.sortlib (or newer version of sorted bbdep)
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This is only one possible way to do this, I am sure there are many others.
 +
 
 +
===USAGE===
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colorRotamers selection
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set_rotamer selection, chi1_angle [,chi2_angle] [,chi3_angle] [,chi4_angle]
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set_phipsi selection phi_angle, psi_angle
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===Scripts (Rotamers.py ; MyMenu.py)===
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<source lang="python">
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</source>
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===EXAMPLES===
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hide lines,all
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hide ribbon
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===SEE ALSO===
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===REFERENCES===
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Dunbrack and Cohen. Protein Science 1997
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[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 03:59, 12 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

Dunbrack Lab Page (Contains backbone-dependent library)