SURFNET - Revision history

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2014-03-28T03:09:10Z

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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.

<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

with

$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

e.g. in a shell on LINUX:

<pre>
$ lx_mapman

MAPMAN > READ map1 gaps.den

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]]

Bosmith at 09:39, 4 August 2006

2006-08-04T09:39:03Z

Bosmith at 09:38, 4 August 2006

2006-08-04T09:38:06Z

Bosmith at 09:27, 4 August 2006

2006-08-04T09:27:56Z

Bosmith at 09:25, 4 August 2006

2006-08-04T09:25:16Z

Bosmith at 09:24, 4 August 2006

2006-08-04T09:24:12Z

Bosmith at 09:20, 4 August 2006

2006-08-04T09:20:08Z

Bosmith at 09:11, 4 August 2006

2006-08-04T09:11:57Z

Bosmith at 09:02, 4 August 2006

2006-08-04T09:02:57Z

Bosmith at 08:30, 4 August 2006

2006-08-04T08:30:39Z

← Older revision		Revision as of 09:25, 4 August 2006
Line 37:		Line 37:
	</pre>		</pre>

−	[[Category:~~Third_Party_Software\|~~Surfaces and Voids]]	+	[[Category:Surfaces and Voids]]

← Older revision		Revision as of 09:24, 4 August 2006
Line 37:		Line 37:
	</pre>		</pre>

−	[[Category:Third_Party_Software]]	+	[[Category:Third_Party_Software\|Surfaces and Voids]]

@@ Line 6: / Line 6: @@
 Asides:
 A. The "endianness" of SURFNET is set to big endian by default - see the
-remarks about the SGI flag.
+remarks about the SGI flag.  Change this if you're on a little endian machine,
 B.SURFNET can be compiled against ccp4 version 5 and 6 libraries
 by following the instructions in the SURFNET distribution and modifiying

@@ Line 4: / Line 4: @@
 <pre>
-Aside: SURFNET can be compiled against ccp4 version 5 and 6 libraries
+Asides:
 by following the instructions in the SURFNET distribution and modifiying
 the link lines at the end of ccp4link.scr to replace

@@ Line 34: / Line 34: @@
 <pre>
-isomesh gaps_mesh gaps 100.0
+isomesh gaps_mesh, gaps, 100.0
 </pre>
 [[Category:Surfaces and Voids]]

@@ Line 3: / Line 3: @@
 . 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 <tt>ccp4link.scr</tt> to replace
+<pre>
 $CLIB/libccp4.a
 with
 $CLIB/libccp4f.a $CLIB/libccp4c.a
-</tt>
+</pre>
 . 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
@@ Line 19: / Line 19: @@
 e.g. in a shell on LINUX:
-<tt>
+<pre>
 $ lx_mapman
@@ Line 25: / Line 25: @@
 MAPMAN > WRITE map1 gaps.xplor XPLOR
-</tt>
+</pre>
 . Open the XPLOR map in PyMol
@@ Line 32: / Line 31: @@
 . 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:
-<tt>
+<pre>
 isomesh gaps_mesh gaps 100.0
-</tt>
+</pre>

@@ 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 [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.
 . Create your surfaces in "CCP4" format in SURFNET.
@@ Line 15: / Line 15: @@
 </tt>
-. Use Gerard Kleywegt's mapman from the USF RAVE package to convert the CCP4 density map to XPLOR format
+. 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:
@@ Line 32: / Line 32: @@
 . 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