Difference between revisions of "SURFNET"

From PyMOLWiki
Jump to: navigation, search
 
Line 1: Line 1:
 
A recipe for reading surfaces from Roman Laskowski's SURFNET program (for finding cavities in macromolecules) into PyMol for visualisation.
 
A recipe for reading surfaces from Roman Laskowski's SURFNET program (for finding cavities in macromolecules) into PyMol for visualisation.
  
Create your surfaces in "CCP4" format in SURFNET.
+
1. Create your surfaces in "CCP4" format in SURFNET.
  
 
Aside: SURFNET can be compiled against ccp4 version 5 and 6 libraries by following the instructions in the SURFNET distribution and modifiying the link lines at the end of ccp4link.scr to replace  
 
Aside: SURFNET can be compiled against ccp4 version 5 and 6 libraries by following the instructions in the SURFNET distribution and modifiying the link lines at the end of ccp4link.scr to replace  
Line 10: Line 10:
  
 
$CLIB/libccp4f.a $CLIB/libccp4c.a
 
$CLIB/libccp4f.a $CLIB/libccp4c.a
 +
 +
2. Use Gerard Kleywegt's mapman from the USF RAVE package to convert the CCP4 density map to XPLOR format
 +
 +
3. Open the XPLOR map in PyMol
 +
 +
4. Generate a mesh or surface object from the map using isomesh or isosurface.

Revision as of 04:24, 4 August 2006

A recipe for reading surfaces from Roman Laskowski's SURFNET program (for finding cavities in macromolecules) into PyMol for visualisation.

1. Create your surfaces in "CCP4" format in SURFNET.

Aside: SURFNET can be compiled against ccp4 version 5 and 6 libraries by following the instructions in the SURFNET distribution and modifiying the link lines at the end of ccp4link.scr to replace

$CLIB/libccp4.a

with

$CLIB/libccp4f.a $CLIB/libccp4c.a

2. Use Gerard Kleywegt's mapman from the USF RAVE package to convert the CCP4 density map to XPLOR format

3. Open the XPLOR map in PyMol

4. Generate a mesh or surface object from the map using isomesh or isosurface.