Difference between revisions of "SURFNET"

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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  
 
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  
  
 +
<tt>
 
$CLIB/libccp4.a  
 
$CLIB/libccp4.a  
 +
</tt>
  
 
with  
 
with  
  
 +
<tt>
 
$CLIB/libccp4f.a $CLIB/libccp4c.a
 
$CLIB/libccp4f.a $CLIB/libccp4c.a
 +
</tt>
  
 
2. Use Gerard Kleywegt's mapman from the USF RAVE package to convert the CCP4 density map to XPLOR format
 
2. Use Gerard Kleywegt's mapman from the USF RAVE package to convert the CCP4 density map to XPLOR format
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e.g. in a shell on LINUX:
 
e.g. in a shell on LINUX:
  
 +
<blockquote><tt>
 
$ lx_mapman
 
$ lx_mapman
 
MAPMAN > READ map1 gaps.den
 
MAPMAN > READ map1 gaps.den
 
MAPMAN > WRITE map1 gaps.xplor XPLOR  
 
MAPMAN > WRITE map1 gaps.xplor XPLOR  
 +
</tt></blockquote>
  
  

Revision as of 04:30, 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.