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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. | ||
| − | + | <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 | ||
| − | |||
with | with | ||
| − | |||
$CLIB/libccp4f.a $CLIB/libccp4c.a | $CLIB/libccp4f.a $CLIB/libccp4c.a | ||
| − | </ | + | </pre> |
| − | 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: | ||
| − | < | + | <pre> |
$ lx_mapman | $ lx_mapman | ||
| + | |||
MAPMAN > READ map1 gaps.den | MAPMAN > READ map1 gaps.den | ||
| + | |||
MAPMAN > WRITE map1 gaps.xplor XPLOR | 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