Changes between Version 118 and Version 119 of Scripts

Timestamp:

Jul 16, 2019, 10:47:51 AM (7 years ago)

Author:

meng

Comment:

--

Scripts

@@ -88 +88 @@
  * [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: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: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:surfsilhouette.py surfsilhouette.py]. Creates silhouette images of surfaces. Tested with Chimera 1.4 daily build September 2, 2009.
+ * [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: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.
@@ -96 +99 @@
  * [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: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: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:quality.py quality.py]. Set the subdivision quality.  Gives smooth appearance to molecule models. Tested with Chimera 1.3. [now settable in Effects tool or with "set" command]
+ * [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.  
 
 = ChimeraX Python Scripts =