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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 | + | <pre> |
| + | 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 | $CLIB/libccp4.a | ||
| − | |||
with | with | ||
| − | |||
$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 | 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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e.g. in a shell on LINUX: | e.g. in a shell on LINUX: | ||
| − | < | + | <pre> |
$ lx_mapman | $ lx_mapman | ||
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MAPMAN > WRITE map1 gaps.xplor XPLOR | MAPMAN > WRITE map1 gaps.xplor XPLOR | ||
| − | </ | + | </pre> |
| − | |||
3. Open the XPLOR map in PyMol | 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. | 4. Generate a mesh or surface object from the map using isomesh or isosurface. | ||
| − | e.g. on the PyMol command line | + | e.g. on the PyMol command line: |
| − | < | + | <pre> |
isomesh gaps_mesh gaps 100.0 | isomesh gaps_mesh gaps 100.0 | ||
| − | </ | + | </pre> |
| + | |||
| + | [[Category:Third_Party_Software]] | ||
Revision as of 09:20, 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