Difference between revisions of "SURFNET"

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1. 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 <tt>ccp4link.scr</tt> to replace  
  
 
$CLIB/libccp4.a  
 
$CLIB/libccp4.a  

Revision as of 04:28, 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

e.g. in a shell on LINUX:

$ lx_mapman MAPMAN > READ map1 gaps.den MAPMAN > WRITE map1 gaps.xplor XPLOR


3. Open the XPLOR map in PyMol

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