We need an overview of phi-psi calculation to be included in the protein
geometry section. What WWW sources can help with this? What other
methods do you recommend? <p> <b>Added by: </b><i>Jeremy Bruce
jbruce@itsa.ucsf.edu</i> <b>on</b> <i>Mo Mar 13 18:02:19 GMT 1995</i> <hr>
(Sorry for the formatting)
Thanks very much, Jeremy - this is exactly the sort of thing that we want
added to the page.
There are two aspects to this question:
- how are phi and psi *defined*. I *think* we have material on this
but if not please would someone volunteer to produce it! :-)
- "how do I calculate phi and psi for my protein?"
The latter requires a program, which could either be interactive or
batch. This is a current problem as I don't think this is universally
available on the course on all platforms. We'd hoped that by this stage
there would be a server running PROCHECK, so that you could drop a
molecule in and it would calculate all the torsions, but I think UCL are
still working on this. I don't think it's possible with RasMol at present.
So - and this is unsatisfactory , but the way the world is at present - I
think you either have to beg a program that works on your device (e.g.
xMol) or find a friend in your institution who has a modelling program.
Does PDB or other servers have anything to offer here?
Suggestions welcome. In principle it is straightforward to write a
simple prog which reads a PDB file and returns geometry. I've done it
and if I had more time I'd try to mount it on a server.
P.