Difference between revisions of "SURFNET"

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A recipe for reading surfaces from [http://www.ebi.ac.uk/~roman/ Roman Laskowski]'s [http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html SURFNET] program (for finding cavities in macromolecules) into PyMol for visualisation.
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A recipe for reading surfaces from [http://www.ebi.ac.uk/~roman/ Roman Laskowski]'s [https://www.ebi.ac.uk/thornton-srv/software/SURFNET/ SURFNET] program (for finding cavities in macromolecules) into PyMol for visualisation.
  
 
1. Create your surfaces in "CCP4" format in SURFNET.
 
1. Create your surfaces in "CCP4" format in SURFNET.
  
 
<pre>
 
<pre>
Aside: SURFNET can be compiled against ccp4 version 5 and 6 libraries  
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Asides:  
 +
A. The "endianness" of SURFNET is set to big endian by default - see the
 +
remarks about the SGI flag.  Change this if you're on a little endian machine,
 +
e.g. LINUX/i386.
 +
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  
Line 15: Line 19:
 
</pre>
 
</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
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2. Use [http://xray.bmc.uu.se/gerard Gerard Kleywegt]'s mapman from the [http://structure.usc.edu/usf/ USF] [http://structure.usc.edu/usf/rave.html RAVE] package to convert the CCP4 density map to XPLOR format
  
 
e.g. in a shell on LINUX:
 
e.g. in a shell on LINUX:
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<pre>
 
<pre>
isomesh gaps_mesh gaps 100.0
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isomesh gaps_mesh, gaps, 100.0
 
</pre>
 
</pre>
  
 
[[Category:Surfaces and Voids]]
 
[[Category:Surfaces and Voids]]
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[[Category:Third_Party_Software|SURFNET]]

Latest revision as of 09:51, 17 January 2018

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.  Change this if you're on a little endian machine, 
e.g. LINUX/i386.
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