= Chimera Python Scripts =

These Python scripts provide capabilities not available using Chimera commands.  They may only work with specific Chimera versions.

 * [attachment:saveunitcell.py saveunitcell.py]. Save unit cell symmetry copies of a molecule.  Tested with Chimera 1.4.  April 26, 2010.
 * [attachment:placeatom.py placeatom.py]. Place a new atom near an existing atom.  Tested with Chimera 1.4.  April 23, 2010.
 * [attachment:square.py square.py]. Square density map values.  Tested with Chimera 1.4.  April 13, 2010.
 * [attachment:capcolor.py capcolor.py]. Set surface cap color.  Tested with Chimera 1.4.  March 5, 2010.
 * [attachment:angle.py angle.py]. Report angle between two axes where each axis is specified by a pair of atoms, for example, axes produced by the "measure rotation" command.  Tested with Chimera 1.4.  Feb 9, 2010.
 * [attachment:surfvol.py surfvol.py]. Report enclosed volumes of each connected piece of a surface, and delete all but the largest piece.  Tested with Chimera 1.5. January 24, 2010.
 * [attachment:closeatoms.py closeatoms.py]. Draw lines between close pairs of selected atoms. Tested with Chimera 1.4. January 14, 2010.
 * [attachment:markeruse.py markeruse.py]. Place markers (spheres) and connect them. Tested with Chimera 1.5 daily build November 24, 2009.
 * [attachment:surfsilhouette.py surfsilhouette.py]. Creates silhouette images of surfaces. Tested with Chimera 1.4 daily build September 2, 2009.
 * [attachment:lightsout.py lightsout.py]. Turns off surface lighting for flat shading. Tested with Chimera 1.4 daily build August 11, 2009.
 * [attachment:xyzsdmap.py xyzsdmap.py]. Makes a volume data set from a text file of xyz points with standard deviations along each axis. Each point is represented as a Gaussian. Tested with Chimera 1.4 daily build August 3, 2009.
 * [attachment:xyzmap.py xyzmap.py]. Makes a volume data set from a text file of xyz points. Each point is represented as a Gaussian. Tested with Chimera 1.4 daily build August 3, 2009.
 * [attachment:pqr2chimera.py pqr2chimera.py]. Split a PQR file into a PDB file that Chimera can read (chimera.pdb) and a [http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/defattr.html defattr file] (chimera.defattr) for assigning the PQR charge attributes if preferred to Chimera charges. Script should be run using Python from a shell rather than inside Chimera.  The defattr may be processed slowly by Chimera due to using "@/serialNumber" selector -- script could be probably be speeded up by moving to ":res@atom" style selectors.  Tested with Chimera 1.4 daily build August 3, 2009.
 * [attachment:surfvert.py surfvert.py]. Writes a text file containing the coordinates of molecular surface vertices and the associated residues. Tested with Chimera 1.4 daily build July 26, 2009.
 * [attachment:markhidden.py markhidden.py]. Places markers at hidden surface vertices.  Used to place markers at centers of hexagons and pentagons of icosahedral lattices made by hkcage command for coloring virus maps. Tested with Chimera 1.4 daily build July 17, 2009.
 * [attachment:interpolate.py interpolate.py]. Interpolate volume data set values at specific points. Tested with Chimera 1.4 daily build July 17, 2009.
 * [attachment:place.py place.py]. Place copies of a model at specified positions and orientations. Tested with Chimera 1.4 daily build July 10, 2009.
 * [attachment:fitnogui.py fitnogui.py]. Fit one map in another and print rotation/translation. Tested with Chimera 1.4 daily build May 18, 2009.
 * [attachment:quality.py quality.py]. Set the subdivision quality.  Gives smooth appearance to molecule models. Tested with Chimera 1.3.
 * [attachment:aniso.py aniso.py]. Anisotropic b-factors shown as ellipsoids for selected atoms using PDB ANISOU records. Tested with Chimera 1.4 daily build July 14, 2009 using PDB 1xy1. [Thermal ellipsoids now available via "aniso" command and Thermal Ellipsoids tool.]
 * [attachment:match.py match.py]. Match chain A of two open molecules and report RMSD and atom pairings to Reply Log. Tested with Chimera 1.3 using PDBs 3fx2 and 1gcn. 
 * [attachment:esp.py esp.py]. Coulombic-ly color all open molecular surfaces. Tested with Chimera 1.4 daily build September 1, 2009 using PDB 3fx2. 
 * [attachment:selLys.py selLys.py]. Select lysine NZ atoms within 8 angstroms of another lysine NZ and put distance monitors between them.  Difficult to do with normal selection language because of no way to exclude the base atoms of a zone selection from the zone test.  Tested with Chimera 1.4 daily build September 21, 2009 using PDB 1www. 
 * [attachment:disulphide.py disulphide.py]. Create disulphide bonds between unprotonated CYS SG atoms that are not already disulphide bonded and that meet reasonable bond-distance criteria.  Tested with Chimera 1.4 daily build November 11, 2009 using PDB 1gc1. 
 * [attachment:dipole.py dipole.py]. Print dipole moment of all open molecular models to the reply log.  The models must already have charges assigned.  Tested with Chimera 1.4 on February 8th, 2010.