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CCP4BB  March 2011

CCP4BB March 2011

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Subject:

Re: Problem with refinement and positive electron density

From:

Eleanor Dodson <[log in to unmask]>

Reply-To:

[log in to unmask][log in to unmask]

Date:

Thu, 3 Mar 2011 10:49:39 +0000

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text/plain

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I think you have been caught by a new REFMAC "feature" which tries  to 
design its own TLS groups including linked H2Os and ligands.

Check your tls output records and see what it has clustered into a group..

I am not sure how to disable this - at times I want to override any 
automatic selection..
Eleanor

On 03/01/2011 07:48 PM, Judith Reeks wrote:
> Dear All,
>
> Thank you for your suggestions. Many of you asked what the occupancies
> were in the region and they were all one, so partial occupancy was not
> the problem.
>
> I was using TLS restraints during the refinement when this problem
> happened. Given the suggestions that TLS may be a problem and that might
> be causing the low B-factors, I went back and re-ran the refinement
> without TLS and the problem disappeared. Then I submitted my latest file
> to the TLSMD server for new restraints and the next round of refinement
> got rid of the problem. The B-factors increased to normal levels (~15
> compared to ~5 before) so it seems to have done the trick.
>
> Thank you to everybody for their help,
>
> Judith Reeks
>
> [log in to unmask]
>
> School of Chemistry
>
> University of St Andrews
>
>
> On 01/03/2011 17:28, Mark Robien wrote:
>> Hmm - kinda interesting
>>
>> In addition to the sorts of things suggested by Mark van Raaij, older
>> versions of Refmac
>> were prone to have a phenomenon with B factors - once they get over a
>> certain level, the algorithm
>> has a very hard time bring them back down, even when the data suggests
>> it.
>>
>> I've usually seen it with much higher B factors than you seem to have
>> here - for example, loops where the B's
>> are actually 40-60, but previous rounds of refinement have the B
>> factors 60-80 or higher.
>> Judging from the coot screen & the residues you are focusing on, I
>> doubt that is the answer (unless you also
>> have a TLS model, in which case I'd wonder). If you do have TLS -
>> well, things get more complicated; for example,
>> is this the edge of a TLS domain?
>>
>> Nonetheless, you could try the solution for the problem that I
>> describe - which is to reset all the B factors to a (very)
>> low B factor - maybe even as low as 2.0 (lower?), and then another
>> round of refmac - with a sufficient number of
>> cycles - will re-refine the B (and xyz), thus escaping the region of
>> refinement space that has a very weak gradient.
>>
>> A variant approach that might be appropriate - similarly reset the B
>> for the (?small) region of your model that has the problem.
>>
>> Sadly, it's been awhile since I did any refinement myself - but the
>> uppsala suite had some of the nicer tools for resetting B within pdb
>> files, without having to do it manually (ugh - not appealing) - or
>> writing an adhoc awk script (a very easy alternative, if you're
>> familiar enough).
>>
>> Mark Robien
>>
>>
>> On 3/1/2011 10:32 AM, Judith Reeks wrote:
>>> Dear All,
>>>
>>> I am currently refining a structure using the latest experimental
>>> version of Refmac (5.6) and there seems to be a problem with my Fo-Fc
>>> map. There is a region where I have fitted residues to the electron
>>> density but after refinement there is still positive electron density
>>> assigned to the region despite the fact that residues fit the
>>> electron density (see link below for a screenshot). Multiple rounds
>>> of refinement have yet to get rid of this problem. I have checked the
>>> PDB file and there does not appear to be any problems with this
>>> region. Has anybody seen something like this before?
>>>
>>> http://i1083.photobucket.com/albums/j382/jreeks/Screenshot2011-03-01at1613402.png
>>>
>>>
>>> Regards,
>>>
>>> Judith Reeks
>>>
>>> [log in to unmask]
>>>
>>> School of Chemistry
>>>
>>> University of St Andrews
>>>
>>
>

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