[ccp4bb]: Summary: refining OCC's of alternate configs

[diane h peapus <dp72@cornell.edu>]

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Hi All:

Thought I'd pass along a summary of a question I asked
a few weeks ago.

Original scenerio:
-----------------
I have alternate configurations of active site contents.
I wanted to know the best way to refine the occupancies
of the 2 different configurations.

Additional info:
The alternate configs come from a reaction in the active
site of the form:  A + B -> C + D, were there is a mixture
of products and unreacted reactants seen.


Summary of answers:
------------------
I got 3 basic answers:

1) Proceed with caution because OCC's and B's are
absolutely coupled and what you choose for one will
effect the other.

2) Use SHELX

3) Use CNS


Comments:
--------

#1 above: #1 above is true, of course.  A method that
someone suggested to exercise this caution is...

>Depending on your resolution, I would opt to only refine B's 
>and adjust the occupancies manually.

With this, you can make an initial guess at the relative
OCC's based on the density, then refine B's.  Presuming
the B's for config_1 and config_2 are similar, you can
manually adjust OCC's until the B's for the 2 configs
are similar to each other.


#3 above:  The authors have told me that they have not 
implimented the option to refine OCC's for alternate configs.  
Many people insisted that you _can_ use CNS, but I think I
believe the authors on this one.

Someone suggested this manual adjust to the CNS limitation:
>I used the alternate conformations feature in CNS to refine 
>my substrate with two different puckers.
>then used the q-group protocul to define the occupancy
>for each conformation. 
>Then manually adjust the occ to be sure it adds up to one.  


But, since my substrate is in the form
   A + B -> C + D
and I know that if A is 80% occupied, then neither C nor D
can be greater than 20%... I can say with firm certainty
that this manual adjust is not accurate.


#2 above:  I have not tried SHELX, but this seems the best 
option for high resolution data.  


that's all...
diane

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