SURFNET: Difference between revisions
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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 | 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 | ||
<tt> | |||
$CLIB/libccp4.a | $CLIB/libccp4.a | ||
</tt> | |||
with | with | ||
<tt> | |||
$CLIB/libccp4f.a $CLIB/libccp4c.a | $CLIB/libccp4f.a $CLIB/libccp4c.a | ||
</tt> | |||
2. Use Gerard Kleywegt's mapman from the USF RAVE package to convert the CCP4 density map to XPLOR format | 2. Use Gerard Kleywegt's mapman from the USF 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: | ||
<blockquote><tt> | |||
$ 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 | ||
</tt></blockquote> | |||
Revision as of 03:30, 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.