This is a read-only mirror of pymolwiki.org
Difference between revisions of "SURFNET"
Jump to navigation
Jump to search
| 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 Roman Laskowski's 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 | 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 | ||
| Line 10: | Line 10: | ||
$CLIB/libccp4f.a $CLIB/libccp4c.a | $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 | ||
| + | |||
| + | 3. Open the XPLOR map in PyMol | ||
| + | |||
| + | 4. Generate a mesh or surface object from the map using isomesh or isosurface. | ||
Revision as of 08:24, 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
3. Open the XPLOR map in PyMol
4. Generate a mesh or surface object from the map using isomesh or isosurface.