Re: [ccp4bb] unknown density

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: What is an aceptable spread in ADP values?
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2010-02-03

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Subject: PDB SEGID Case Sensitivity
From: James Stroud xtald00d {- at -} GMAIL {- dot -} COM
Date: 2010-02-03

Subject: Re: unknown density
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2010-02-03

Mark J. van Raaij wrote:
> as it appears to bear near the guanidine group of an arginine, I would
> suggest it is a partially occupied and disordered sulphate and/or
> phosphate.
> whether this is practically modellable is another matter, a sulphate at
> occ. 0.5 is an option, or putting a water with a remark in the pdb that
> this water is really modelling partially occupied and disordered
> sulphate and/or phosphate.

I've found that remarks in PDB files are quite useless. If you label
an atom as a water molecule, every program that reads that file will make
the assumption that you believed a water molecule was there. Even most
humans will fail to dig into the header of the PDB file to see if you
had some specific comment about that particular atom.

Since the PDB file is your interpretation of the electron density,
and the electron density will be available to anyone who wants it, I
don't see the point of marking a spot with a dummy atom when you don't
have an interpretation.

As for developing an interpretation: I've had good success in
cleaning up such maps using Buster. You don't need to add dummy
waters in the refinement to remove "vacuum bias", just leave it
alone while you fix everything you can figure out.

Dale Tronrud

> Mark
>
> Quoting Katja Schleider :
>
>> Dear all,
>>
>> I found some fairly substantial density in the active site of my
>> protein structure. But I don´t know what it should be. My
>> crystallisation condition consists of lithium sulfate,
>> citrate-phosphate and peg1000. The whole lot doesn't make a dashed
>> bit of sense! Any suggestions to fill this density with something?
>> Picture is attached.
>>
>> Thanks a lot,
>>
>> Katja
>>
>>
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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: What is an aceptable spread in ADP values?
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2010-02-03

Next message:
Subject: PDB SEGID Case Sensitivity
From: James Stroud xtald00d {- at -} GMAIL {- dot -} COM
Date: 2010-02-03