[phenixbb] multiple ligand conformations

Pavel Afonine pafonine at lbl.gov
Sat Nov 19 23:28:13 PST 2011

Hi Len,

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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