[ccp4bb] shelxl, refinement of occupany

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CCP4bb <-- 2007 <-- March 2007 <-- 21 March 2007

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Subject: Re: Highest shell standards
From: Ulrich Genick genick {- at -} BRANDEIS {- dot -} EDU
Date: 2007-03-21

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Subject: Re: modelling with sad/mad data
From: Peng Zhang pzhang {- at -} SIBS {- dot -} AC {- dot -} CN
Date: 2007-03-21

Subject: shelxl, refinement of occupany
From: U Sam us_x {- at -} HOTMAIL {- dot -} COM
Date: 2007-03-21

I am looking for some advice.

(1) In shelex what should I mention to refine occupancy.
I have two molecule in asym unit.
In A molecule residues 89-92 is present, but in B these residues are
missing.
So I believe in B these residues should not be with zero occupancy, although
I donot find any prominent density (Fo-Fc). Occupancy could be anywhere
between 0.0 to 1.0. How can I refine this parameter. Or, I should neglect
this missing part of residues in B indicating a occupancy of 0.0 or keep a
gap of these residues with no information including coordinates.

Right now R1=14% and R1(free) =18%, without making water anisotropic.

(2) I am using 1.4 A data. Should I refine water anisotropically ? If answer
is yes, when.

(3) Should I add hydrogen at this resolution. If yes, when should I do.

Thanks
Sam

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CCP4bb navigation

CCP4bb <-- 2007 <-- March 2007 <-- 21 March 2007

Previous message:
Subject: Re: Highest shell standards
From: Ulrich Genick genick {- at -} BRANDEIS {- dot -} EDU
Date: 2007-03-21

Next message:
Subject: Re: modelling with sad/mad data
From: Peng Zhang pzhang {- at -} SIBS {- dot -} AC {- dot -} CN
Date: 2007-03-21