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.
this could be achieved by using a ChemObject/Atom property, something like
The property name could be chosen better, but that does not matter that
by default the first conformation is copied on reading to the Atom's actual
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...
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...
PhD on Molecular Representation in Chemometrics