Re: [Jmol-developers] disappearing atoms?

[timothy d. <mol...@ma...>]

Miguel sent (2004.06.02 at 4.52p [+0200gmt]) :

>
>>>It is currently not implemented, but I plan to put in a
>>>restriction that an 'animation' needs to contain the same number
>>>and the same elements in the same order in every model.
>>>
>>>Q: Would this type of restriction conflict with any of these
>>>applications?
>>>
>>>(The only thing I can think of is nuclear reactions ... where the
>>>atom type would change :-)
>>>
>>
>>unless I misunderstand your suggestion, I would argue against such
>>a restriction.  it is often helpful to animate the transition from
>>bound to unbound states of an enzyme, for example, where the bound
>>state structure contains ligand but the unbound state does not.
>
>But the atoms still exist, right?
>
not necessarily.  generally a macromolecular animation file is
constructed by merging the atom records of the macromolecule without
ligand, and the atom records of the macromolecule plus ligand.  so two
different crystal structures combined into one file and set off by MODEL
'tags'.

there are cases where it is more than two structures as well - for
example, unbound pre-reaction structure, bound intermediate, unbound
post-reaction structure.

the merged files can be edited by hand; for example, adding a ligand to
the unbound structure and just not showing it.  but will that be a
problem when calculating connectivity?  especially if the ligand
overlaps the unbound structure?  it has been an issue in the past, in
Chime, and the way around it has been to address 'conflicts'
atom-by-atom using script commands.


regards,

tim
--=20
Timothy Driscoll
molvisions - see, grasp, learn.
<http://www.molvisions.com/>
usa:north carolina:wake forest