This is a read-only mirror of pymolwiki.org

Difference between revisions of "SURFNET"

From PyMOL Wiki
Jump to navigation Jump to search
 
m (14 revisions)
 
(13 intermediate revisions by one other user not shown)
Line 1: Line 1:
A recipe for reading surfaces from Roman Laskowski's SURFNET program (for finding cavities in macromolecules) into PyMol for visualisation.
+
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.
  
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 ccp4link.scr to replace  
+
<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
 +
</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
 +
 +
e.g. in a shell on LINUX:
 +
 +
<pre>
 +
$ lx_mapman
 +
 +
MAPMAN > READ map1 gaps.den
 +
 +
MAPMAN > WRITE map1 gaps.xplor XPLOR
 +
</pre>
 +
 +
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:
 +
 +
<pre>
 +
isomesh gaps_mesh, gaps, 100.0
 +
</pre>
 +
 +
[[Category:Surfaces and Voids]]
 +
[[Category:Third_Party_Software|SURFNET]]

Latest revision as of 03:09, 28 March 2014

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