Bob,
If Resolver does not get a connectivity identifier (e.g. taxol), it relies on
database look up (multi databases, including PubChem). I have no idea what the
priority is, nor what identifier Resolver seeks if it gets a non IUPAC name.
But let’s assume it goes to PubChem and seeks the SMILES. PubChem lists taxol
under paclitaxel, and the paclitaxel listing lists 3D status as, "Conformer
generation is disallowed since too many atoms.” OK, grab the SMILES, go back to
Resolver, and give this SMILES to CORINA, Resolver’s engine.
A few weeks ago we were talking about Jmolers always using Taxol as a test
molecule, so I took the PubChem SMILES and hand entered it into Resolver. If
you give the PubChem taxol SMILES to Resolver, all the king’s horses and all
the kings men cannot put taxol’s ensembles back together again! So, yes, I
guess some limit is in place on Resolver also.
I used to think that PubChem used MMFF94. It came out in Bob Bellford's on line
cheminformatics course that PubChem uses a special version of MMFF94. It would
be interesting to find out what the atom number limits are on PubChem and
Resolver. I’ll check both.
Otis
PS
Bob really had a powerhouse faculty of that course - who’s who of
cheminformatics.
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On Mar 22, 2016, at 2:54 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>
>
> On Tue, Mar 22, 2016 at 11:05 AM, Otis Rothenberger <osrot...@icloud.com
> <mailto:osrot...@icloud.com>> wrote:
> Hi Richard,
>
> That model is coming from Resolver. Resolver does not use MM to compute 3d
> models. Basically, the steps are as follows:
>
> 1) The connection identifier (SMILES, InChI, IUPAC, etc) is broken down into
> fragments called ensembles. Fixed geometries for these fragments exist in
> memory.
> 2) The ensembles are reassembled carrying their fixed geometry into the final
> SDF.
>
>
> I did not know that! Thank you, Otis. So perhaps the problem with taxol is
> that it doesn't have some sort of fragment it needs?
>
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