great. Yes, that was what I was after. I just added psi and phi to
"getproperty polymerInfo" so in principle, if one wanted to do this sort
of thing with Jmol, one could.
We need to think about revising how Jmol calculates helix structure. I
think it is over-assigning helix structure based on the simple algorithm:
return (phi >= -160) && (phi <= 0) && (psi >= -100) && (psi <= 45);
where psi is for the residue in question, and phi is for the next
residue in line in the direction of the C terminus.
Q: What is the origin of this calculation (Tim?)
What this is doing is assigning as helix many residues that Rasmol and
Astex and whatever is used in CIF generation call turns. It seems overly
broad. What seems to be happening (for example, in 2hhd) is that helixes
with large swings in psi are being counted as single helixes. You might
not notice this when using Cartoons, but with Rockets, it is quite
obvious that something is wrong, because rockets have to go from one end
of a helix to the other directly. This is what Angel noticed.
My preliminary fix is to temporarily assign two sorts of helix: ones for
which (phi < 0 and psi < 25) and one for which that is not true. This
forces a kink in a standard helix to close that helix and start another.
This temporary assignment is for the algorithm only, not anything else
-- in any other terms, a helix is a helix (so far).
Rolf Huehne wrote:
>Bob Hanson wrote:
>
>
>>Does anyone know of a website that lets you indicate any PDB file and then
>>
>>1) show the Ramachandran plot
>>
>>and, preferably,
>>
>>2) allow clicking on the plot to see which residues are involved?
>>
>>
>>
>>
>The 'AstexViewer' from MSD at the EBI. It is a java applet.
>In the 'Graphs' menu there is a 'Rama' entry and you get an interactive
>window where you can click on a spot in the ramachandran plot and the
>corresponding residue is shown and in the structure viewer it is
>centered and zoomed in on it.
>
>It should work with any PDB code, for example:
>
>http://www.ebi.ac.uk/msd-srv/apps/Viewer/ViewerServlet?id=1deh
>
>Regards,
>Rolf
>
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