Difference between revisions of "SURFNET"

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A recipe for reading surfaces from Roman Laskowski's 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.
  
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  
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<pre>
 +
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  
 
$CLIB/libccp4.a  
Line 10: Line 17:
  
 
$CLIB/libccp4f.a $CLIB/libccp4c.a
 
$CLIB/libccp4f.a $CLIB/libccp4c.a
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</pre>
  
2. Use Gerard Kleywegt's mapman from the USF 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:
  
 +
<pre>
 
$ lx_mapman
 
$ lx_mapman
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MAPMAN > READ map1 gaps.den
 
MAPMAN > READ map1 gaps.den
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MAPMAN > WRITE map1 gaps.xplor XPLOR  
 
MAPMAN > WRITE map1 gaps.xplor XPLOR  
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</pre>
  
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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.
  
3. Open the XPLOR map in PyMol
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e.g. on the PyMol command line:
 +
 
 +
<pre>
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isomesh gaps_mesh, gaps, 100.0
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</pre>
  
4. Generate a mesh or surface object from the map using isomesh or isosurface.
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[[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