Re: [ccp4bb] Lots of noise in structure

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

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Date: 2010-01-06

Subject: Re: Lots of noise in structure
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2010-01-06

In addition to what the others have mentioned, if you're curious about sigma
levels to contour you may want to deliberately omit
an atom from your structure (say an ordered oxygen in a good portion of the
structure) - the height of the difference density peak would be meaningful
and you then could roughly judge whether your other peaks are garbage or
not.

Artem

On Wed, Jan 6, 2010 at 9:00 AM, Artem Evdokimov
wrote:

> In addition to what the others have mentioned, if you're curious about
> sigma levels to contour you may want to deliberately omit
> an atom from your structure (say an ordered oxygen in a good portion of the
> structure) - the height of the difference density peak would be meaningful
> and you then could roughly judge whether your other peaks are garbage or
> not.
>
> Artem
>
> On Wed, Jan 6, 2010 at 12:21 AM, Rajan wrote:
>
>> Dear All,
>>
>> Happy New Year
>>
>> I am working with a 2.06 Ang resolution structure in F432 space group and
>> further using REFMAC (also tried Phenix) program for refinement of my
>> model.
>>
>> Every thing in the structure seems good, R factor/ R free= 18.59/20.77 but
>> the structure is too noisy (blobs of difference Fourier with red as well as
>> green density).
>>
>> As such electron density is looking good for the protein part.
>>
>> Is there any parameter which i had to check.
>>
>> Thanking you in advance
>>
>> Rajan
>>
>> --
>> ************************************************
>> Current Address:
>>
>> Rajan Vyas
>> Research Scholar
>> Deptt. of Biotechnology
>> Panjab University Chandigarh, India
>> 160014 Mob. +919417374197
>> Fax: +91-172-2625254
>> ************************************************
>>
>
>

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