[phenixbb] Question about restraints in individualB-factor re finement

Schubert, Carsten [PRDUS] CSCHUBER at prdus.jnj.com
Fri May 25 10:10:21 PDT 2007

Thanks Pavel,Nigel:

so it looks as if neither approach works and I would need to split the
ligands into seperate PDB files for a truly independent B-factor refinement.

Thanks for the hint about the non-bonded interactions. That was useful.



-----Original Message-----
From: phenixbb-bounces at phenix-online.org
[mailto:phenixbb-bounces at phenix-online.org]On Behalf Of Pavel Afonine
Sent: Friday, May 25, 2007 12:51 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Question about restraints in individualB-factor

Hi Carsten,

for the refinement of b-factors there is no difference between two options.
We use the sphere b-factors restraints which are calculated based on
interatomic distances and the information about alternative conformations is
not used at that point.

However if you refine the coordinates, the difference is significant: if you
refine it as two separate residues then they will "see" each other for
non-bonded interactions term calculation and hence will be pushed apart.

Please let me know if you still have questions!

Schubert, Carsten [PRDUS] wrote: 
I have a question about the handling of restraints in the individual
B-factor refinement routine. 
What I'd like to do is to refine a ligand, which can be present in 2 or more
different conformations/orientations in its binding site. I'd like to use
B-factor refinement on the various instances of the ligand, which one is the
most relevant one, assuming that the most relevant conformation/orientation
is associated with the lowest B-factor (Validity of that assumption set
aside ...)
My question is now is there any difference in the restraints applied to the
b-factors in the scenarios where A) the ligand is modeled as alternate
conformations i.e.
ATOM   2724  C01AINH I   1      27.808  26.376  23.301  0.50 27.77      I
ATOM   2733  C01BINH I   1      30.898  22.496  17.340  0.50 22.15      I
vs. scenario B) where the same ligand is modeled as 2 different residues 
ATOM   2724  C01 INH I   1      27.808  26.376  23.301  0.50 27.77      I
ATOM   2733  C01 INH I   2      30.898  22.496  17.340  0.50 22.15      I
Basically, what I am trying to achieve is to uncouple the B-factor
refinement of each individual instance of the ligand from its other
instance(s). Are there any hidden pitfalls between these 2 scenarios I
should be aware of?

Many thanks for any input. 


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