[Jmol-developers] Joint the dots and covalent radii

[Peter Murray-R. <pm...@ca...>]

At 16:14 24/04/2004 +0200, Miguel Howard wrote to OpenBabel list:
 >PMR wrote:
 > > - joint the dots with covalent radii (NB I think Jmol may make rather
 >too
 > > many bonds here. I will post.to Jmol separately
 >
 >Jmol should be using the same algorithm as OpenBabel. And the covalent
 >radii values are taken from OpenBabel.

Thanks. We have been analysing our MOPAC calculations and displaying the
results in Jmol. See:
http://wwmm.ch.cam.ac.uk/moin/ProteusMolecules
These are molecules which change their connection table between the input
and output of MOPAC. MOPAC does not output bonds so we used our own
algorithm to join atoms (we will probably use CDK for consistency).
***What we would like to do is use a set of given bonds rather than have
Jmol calculate its own.*** This is demonstrated in:
http://wwmm.ch.cam.ac.uk/download/mopac/nci_proteus/nsc5220_view.html
where the input molecule is truly horrible and MOPAC rescues it. The input
bonds are given and we would like to show them, not the join-the-dots
result. If Jmol does this, what is the switch, else can it be easily fixed?
Thanks
P.




Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069