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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. | + | 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. |
1. Create your surfaces in "CCP4" format in SURFNET. | 1. Create your surfaces in "CCP4" format in SURFNET. | ||
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</tt> | </tt> | ||
| − | 2. Use Gerard Kleywegt's mapman from the USF 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 |
e.g. in a shell on LINUX: | e.g. in a shell on LINUX: | ||
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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. isomesh gaps_mesh gaps 100.0 | + | e.g. on the PyMol command line |
| + | |||
| + | <tt> | ||
| + | isomesh gaps_mesh gaps 100.0 | ||
| + | </tt> | ||
Revision as of 09:11, 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