It's a run-away animation. I will look at it this evening.
On Sun, Dec 1, 2013 at 12:05 PM, Angel Herráez <[email protected]> wrote:
> Hi all
> I ma trying to align two related molecules base on the subset of common
> atoms. For some pairs it works, but for others the reported RMSD is zero
> and
> when I try to move one of the models ot vanishes and Jmol hangs, does not
> accept any more input.
> Using Jmol application, I've tried several versions from 13.1.9 to
> 13.3.9_2013.11.27d
>
> Models are attached. My script is:
>
> load sofosbuvir.mol
> load append sofosbuvir_pa-0.mol
> compare {2.1}{1.1} // ok
> compare {2.1}{1.1} subset {atomno<16} // reports RMSD=0
> compare {2.1}{1.1} subset {atomno<16} rotate translate // failure
>
> Thanks for any hints and specially for an alternative (this is for MP and
> I'd
> rather stick to the currently installed version, 13.1.9)
>
> (I also tried using the SMILES option, but I am unable to find the correct
> expression and syntax.)
>
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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