Re: [ccp4bb] fixing position in the refinement: Shelx, refmac5

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Subject: Re: fixing position in the refinement: Shelx, refmac5
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-04-04

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From: Jovine Luca luca {- dot -} jovine {- at -} KI {- dot -} SE
Date: 2008-04-04

Subject: Re: fixing position in the refinement: Shelx, refmac5
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-04-04

No. Better way is restraining internal degrees of freedom. Something
like elastic network model:
Tirion MM (1996) Phys Rev Letters 77 pp 1905-1908

But care should be taken with weights and which distances should be
restrained.

Fiixing position is not good way of using prior information (In my
view of course, which is debatable)

Garib

On 4 Apr 2008, at 06:56, Frank von Delft wrote:

> Is that also how you would restrain refinement at low resolution
> when using a high-resolution model? (e.g. a 1.8A model into 4A data)
>
> phx.
>
>
>
> Garib Murshudov wrote:
>> In newer version of refmac you can use harmonic restraints. Take
>> the new stable version of refmac from
>> www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
>>
>> and use harmonic restraints as described in:
>> http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html
>>
>>
>> Keyword is:
>>
>> external harmonic residues from [residue_number] [chain_name] to
>> [residue_number] [chain_name] sigma [value] sigma 0.1
>>
>>
>> With the current ccp4i version you can use developers option and
>> add an external keyword file that contains this keyword for
>> residues you want to fix.
>>
>> I hope it helps.
>>
>> Garib
>>
>> On 4 Apr 2008, at 00:39, U Sam wrote:
>>> How one can fix position of few residues when refining in SHELX
>>> or Refmac5.
>>> Thanks. Sam.
>>> _________________________________________________________________
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>>
>

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CCP4bb <-- 2008 <-- April 2008 <-- 04 April 2008

Next message:
Subject: Re: OMIT map from Sfcheck
From: Jovine Luca luca {- dot -} jovine {- at -} KI {- dot -} SE
Date: 2008-04-04