On Thursday 20 November 2003 12:11, timothy driscoll wrote:
> at 11:46 am EDT on (Thursday) 20 November 2003 E.L. Willighagen said:
> > On Thursday 20 November 2003 11:28, timothy driscoll wrote:
> > > > > There is currently not a good mechanism in Jmol to support
> > > > > alternate locations. Therefore, I will modify the .pdb reader to
> > > > > take the first conformation it sees and discard the others.
>
> [...]
>
> > In the latter case, it would require Jmol to mark an Atom with two
> > coordinate sets... this is still doable, but Miguel and I need to have
> > a very clear picture then what is intended... he's not a chemist, but I
> > am, so I think we can work this out... even pretty quickly...
>
> I will defer to the true chemists, but this sounds like the cleanest and
> most logical option to me.
Miguel,
this could be achieved by using a ChemObject/Atom property, something like
("org.openscience.cdk.io.pdb.alternativeConformation.A", Point3d)
and (etc)
("org.openscience.cdk.io.pdb.alternativeConformation.B", Point3d)...
The property name could be chosen better, but that does not matter that
much...
by default the first conformation is copied on reading to the Atom's actual
coordinates: Atom.point3d
After that, the script command "select bla;B" will copy the property
"org.openscience.cdk.io.pdb.alternativeConformation.B" content (of type
Point3d) directly into the Atom.point3d field... and since we have a copy of
the A conformer too, we can restore the old situation...
Miguel, others,
does that sounds reasonable?
> > So, my main question right now is, how do you use the alternative
> > conformations of residues? Is there a webpage with Rasmol/Chime script,
> > or some other demo that would examplify how the script commands are
> > used and what effect they give... this will help me identify the best
> > internal representation (one of the two options...)...
>
> unfortunately I do not have a Web page demonstrating this. I am not sure
> that Chime even supports alt conf, though I will check as soon as I can...
Please do.
kind regards,
Egon
--
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Nijmegen University
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