[phenixbb] multiple ligand conformations
pafonine at lbl.gov
Sat Nov 19 23:28:13 PST 2011
sorry for delayed reply - somehow I managed to overlook your email...
> One of the groups here has run into a problem in the refinement of
> their structure or more specifically a ligand bound to the structure.
> Through a series of other experiments they know that a photo reaction
> occurs to the compound when exposed to high flux as found at your
> everyday synchrotron source. The exposure changes the bonding such
> that there are two conformations with a bit in between obviously.
> They collected 360 degrees worth of data and if the data is split you
> can model the two conformations depending which half of the data you
> use. They are trying to refine with all of the data and modeling of
> the ligand into the two conformations. In refmac they can model this
> with no problem but in Phenix the ligand adopts a chemically wrong
> conformation, sort of a halfway point between the two chemically
> relevant conformations. They have used Phenix to do similar
> refinements on other structures but it appears either the last release
> or the latest release is causing problems. They have started out with
> everything from 50% occupancy to shifting it towards on one
> conformation or the other and the ligand always ends up in the
> chemically wrong position. Data is in the 1.4-1.5 ang. range.
It's hard to tell what's causing this without looking at actual files.
But I'm pretty sure it must be something easy to fix. If you send me an
example: a fraction of PDB file containing atoms in question, and
explain how you expect their occupancies to be refined, then I will send
you back a working example and explain why it did not work before.
I will look into it immediately once I have the files.
P.S.: Please send the files to my email, not to the whole mailing list.
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