Re: [ccp4bb] Lots of noise in structure

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

Previous message:
Subject: Re: Anions in protein structures
From: Stephen Graham scg34 {- at -} CAM {- dot -} AC {- dot -} UK
Date: 2010-01-06

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Subject: Cavity filling
From: Simon Kolstoe s {- dot -} kolstoe {- at -} UCL {- dot -} AC {- dot -} UK
Date: 2010-01-06

Subject: Re: Lots of noise in structure
From: "Soisson, Stephen M" stephen_soisson {- at -} MERCK {- dot -} COM
Date: 2010-01-06

Rajan,

I'll second what Eleanor and George have said - high symmetry space
groups with noisy Intensity measurements (perhaps it was a weak data set
with high Rmerge?) really exaggerates the amount of "garbage" that you
see in the maps.

Cheers-

Steve

________________________________

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Rajan
Sent: Wednesday, January 06, 2010 1:22 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Lots of noise in structure

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

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Rajan Vyas
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Deptt. of Biotechnology
Panjab University Chandigarh, India
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CCP4bb navigation

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

Previous message:
Subject: Re: Anions in protein structures
From: Stephen Graham scg34 {- at -} CAM {- dot -} AC {- dot -} UK
Date: 2010-01-06

Next message:
Subject: Cavity filling
From: Simon Kolstoe s {- dot -} kolstoe {- at -} UCL {- dot -} AC {- dot -} UK
Date: 2010-01-06