Difference between revisions of "SURFNET"

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<pre>
 
<pre>
Aside: SURFNET can be compiled against ccp4 version 5 and 6 libraries  
+
Asides:  
 +
A. The "endianness" of SURFNET is set to big endian by default - see the
 +
remarks about the SGI flag.
 +
B.SURFNET can be compiled against ccp4 version 5 and 6 libraries  
 
by following the instructions in the SURFNET distribution and modifiying  
 
by following the instructions in the SURFNET distribution and modifiying  
 
the link lines at the end of ccp4link.scr to replace  
 
the link lines at the end of ccp4link.scr to replace  

Revision as of 05:38, 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.

Asides: 
A. The "endianness" of SURFNET is set to big endian by default - see the 
remarks about the SGI flag.
B.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.

e.g. on the PyMol command line:

isomesh gaps_mesh, gaps, 100.0