Changes between Version 14 and Version 15 of Scripts


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Timestamp:
Aug 5, 2009, 10:29:33 AM (17 years ago)
Author:
goddard
Comment:

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  • Scripts

    v14 v15  
    33These Python scripts provide capabilities not available using Chimera commands.  They may only work with specific Chimera versions.
    44
     5 * [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.
     6 * [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.
    57 * [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.
    68 * [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.
    … …  
    1113 * [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.
    1214 * [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.
    13  * [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.