Hi all,
In the past couple of years, Mark Harris in Uppsala has developed a bunch of
programs and servers that are useful for crystallographers, structural
biologists and structural bioinformaticians. Some of his programs are listed
here:
http://xray.bmc.uu.se/markh/programs.html
My favourite is "O on a stick" for Macs. If you download a tarball from an EDS
entry, you can unzip it and drop it on the "O on a stick" icon on your desktop
and O will start up and execute a bunch of macros. Within seconds you have the
PDB entry and the EDS maps on your screen, ready for scrutiny!
Mark's servers are listed here:
http://xray.bmc.uu.se/markh/servers.html
Several of these provide a user-friendly interface to some of my old programs:
- Australis allows you to do a quick and dirty superposition of two protein
structures, and it will show the result in Jmol as well as allow you to
download the superimposed coordinates, structure-based sequence alignment,
etc. Australis is driven by LSQMAN.
- Borealis does essentially the same as Australis, but for nucleic acid
structures instead of proteins (try out the default example, 1HR2 versus
1U9S). Borealis is also driven by LSQMAN.
- Spasm is a server to run SPASM (unsurprisingly, perhaps) which allows you to
detect small motifs (that you provide) in existing PDB entries. Use the
default example to find out how it works.
- Spana runs a program that I've never even published, SPANA - it does the
same as SPASM, but for nucleic acid motifs and structures. Use the default
example to find out what it can do.
- CavitySearch can be used to find cavities and tunnels in proteins. It can
use either VOIDOO or MAMA (implementing Delaney's method). You can download
the results and view the cavity(ies) with the AstexViewer. Try 1CEL chain A,
looking for the biggest cavity using Delaney's method - this shows how a
tunnel in a structure can be visualised. See also:
http://xray.bmc.uu.se/usf/vis_tunnel.html
- Morphtician allows you to do simple morphs between protein chains in the
same or different structures. It uses LSQMAN under the hood. Interpolated
coordinates can be downloaded and the morphing visualised in Jmol. See also:
http://xray.bmc.uu.se/usf/mol_morph.html
- ValLiGURL has been around for a few years.
Note: since Mark is no longer employed at Uppsala University, these programs
and servers come with no warranty or support.
--Gerard
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Gerard J. Kleywegt
http://xray.bmc.uu.se/gerard mailto:[email protected]
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The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
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Little known gastromathematical curiosity: let "z" be the
radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
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