[ccp4bb] exclude NCS regions in phenix.refine

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

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From: Takanori Otomo totomo {- at -} SCRIPPS {- dot -} EDU
Date: 2009-03-02

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Subject: Re: Twin refinement not working in CCP4 6.1.1
From: Charles Ballard charles {- dot -} ballard {- at -} STFC {- dot -} AC {- dot -} UK
Date: 2009-03-03

Subject: exclude NCS regions in phenix.refine
From: "Van Den Berg, Bert" Lambertus {- dot -} VandenBerg {- at -} UMASSMED {- dot -} EDU
Date: 2009-03-02

Hello all,

I'm refining a structure with 4 molecules in the AU. The molecules have substantial differences in certain regions, so I want to exclude those regions from the NCS restraints calculation and usage. How do i do this? As far as I can see, by selecting residues via for example "chain A and (resseq 20:50 or resseq 88:299), etc" the NCS restraints are calculated from the specified part of the molecules but still applied to the entire molecules, which I don't want.

Thanks for any hints!

Bert van den Berg
University of Massachusetts Medical School
Program in Molecular Medicine
Biotech II, 373 Plantation Street, Suite 115
Worcester MA 01605
Phone: 508 856 1201 (office); 508 856 1211 (lab)
e-mail: bert.vandenberg@umassmed.edu
http://www.umassmed.edu/pmm/faculty/vandenberg.cfm

-----Original Message-----
From: CCP4 bulletin board on behalf of Artem Evdokimov
Sent: Fri 2/27/2009 7:00 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Off topic: Mammalian gene expression in E. coli

Hello,

The short answer is 'yes'. If you can use both methods :) The issue with
limited proteolysis lies in the questionable state of the full-length
protein - if the stuff is nasty and misfolded, then fagments generated by
proteolytic digest aren't going to be meaningful. On the other hand if you
have a small amount of decent quality full-length protein, digest can be
extremely useful. Deuterium exchange is a nice technique if one of your
friends is an altruistic mass-spectroscopist :)

Purely theoretical methods are limited as well, especially if you're working
with a bunch of unknown domains in a sequence that has low identity with
anything that has associated structures. And in the end, even for known
structures (or very similar ones) truncation can generate surprises - both
positive and negative ones.

Artem

>Hi:
>I am following this with interest. Nice and useful info.
>My question is: how do you "chop the protein into useful hunks"?
>Using some domain identifying software or using limited proteolysis?
>Thanks
>Subbu

CCP4bb navigation

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

Previous message:
Subject: Postdoc position
From: Takanori Otomo totomo {- at -} SCRIPPS {- dot -} EDU
Date: 2009-03-02

Next message:
Subject: Re: Twin refinement not working in CCP4 6.1.1
From: Charles Ballard charles {- dot -} ballard {- at -} STFC {- dot -} AC {- dot -} UK
Date: 2009-03-03