Re: [ccp4bb] unknown density

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

Previous message:
Subject: Re: unknown density
From: Bostjan Kobe b {- dot -} kobe {- at -} UQ {- dot -} EDU {- dot -} AU
Date: 2010-02-03

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Subject: Re: PDB SEGID Case Sensitivity
From: Vellieux Frederic Frederic {- dot -} Vellieux {- at -} IBS {- dot -} FR
Date: 2010-02-04

Subject: Re: unknown density
From: "Mayer, Mark (NIH/NICHD) [E]" mayerm {- at -} MAIL {- dot -} NIH {- dot -} GOV
Date: 2010-02-03

I'd support BR's position. Why the compelling urge to fill every blob with atoms? Density should only be modeled when its interpretable. One can comment about the blob in a paper, and perhaps even show maps for the region, indicating that there might be something there if its believed to be a functionally important region. One could deposit without building in this site, but say that combinations of disorder ions/water etc all fit the density equally well.
________________________________________
From: Bostjan Kobe [b.kobe@UQ.EDU.AU]
Sent: Wednesday, February 03, 2010 8:01 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] unknown density

I think there is at least one more option here (relevant at least in some rare cases):
Identifying what that something is likely to be can be significant and may advance your career

Of course it is important to present supporting or otherwise evidence for the interpretation. As already discussed, this is difficult in a PDB file, and that’s why the accompanying publication can be very important.

Bostjan

On 4/02/10 3:54 AM, "Bernhard Rupp" wrote:

General remark – if I may
Putting nothing in:
no significant effect on model and life in general
Putting ‘something’ potentially wrong and misleading in:
could be detrimental to your career

BR

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Katja Schleider
Sent: Wednesday, February 03, 2010 9:18 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] unknown density

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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Bostjan Kobe
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School of Chemistry and Molecular Biosciences
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CCP4bb navigation

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

Previous message:
Subject: Re: unknown density
From: Bostjan Kobe b {- dot -} kobe {- at -} UQ {- dot -} EDU {- dot -} AU
Date: 2010-02-03

Next message:
Subject: Re: PDB SEGID Case Sensitivity
From: Vellieux Frederic Frederic {- dot -} Vellieux {- at -} IBS {- dot -} FR
Date: 2010-02-04