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 <tt>ccp4link.scr</tt> to replace  
+
<pre>
 +
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  
  
<tt>
 
 
$CLIB/libccp4.a  
 
$CLIB/libccp4.a  
</tt>
 
  
 
with  
 
with  
  
<tt>
 
 
$CLIB/libccp4f.a $CLIB/libccp4c.a
 
$CLIB/libccp4f.a $CLIB/libccp4c.a
</tt>
+
</pre>
  
 
2. Use [http://xray.bmc.uu.se/gerard Gerard Kleywegt]'s mapman from the [http://alpha2.bmc.uu.se/usf/ USF] [http://alpha2.bmc.uu.se/usf/rave.html RAVE] package to convert the CCP4 density map to XPLOR format
 
2. Use [http://xray.bmc.uu.se/gerard Gerard Kleywegt]'s mapman from the [http://alpha2.bmc.uu.se/usf/ USF] [http://alpha2.bmc.uu.se/usf/rave.html 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:
  
<tt>
+
<pre>
 
$ lx_mapman
 
$ lx_mapman
  
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MAPMAN > WRITE map1 gaps.xplor XPLOR  
 
MAPMAN > WRITE map1 gaps.xplor XPLOR  
</tt>
+
</pre>
 
 
  
 
3. Open the XPLOR map in PyMol
 
3. Open the XPLOR map in PyMol
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4. Generate a mesh or surface object from the map using isomesh or isosurface.
 
4. Generate a mesh or surface object from the map using isomesh or isosurface.
  
e.g. on the PyMol command line
+
e.g. on the PyMol command line:
  
<tt>
+
<pre>
 
isomesh gaps_mesh gaps 100.0
 
isomesh gaps_mesh gaps 100.0
</tt>
+
</pre>
 +
 
 +
[[Category:Third_Party_Software]]

Revision as of 05:20, 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.

e.g. on the PyMol command line:

isomesh gaps_mesh gaps 100.0