Re: [ccp4bb] exclude NCS regions in phenix.refine

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

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Subject: Re: exclude NCS regions in phenix.refine
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-03-03

Hi Bert,

- define NCS selections in your input parameters file "ncs.txt" (just
copy-paste-edit whatever is defined automatically, for example);
- do not forget to use "main.ncs=true";
- turn off automatic NCS detection: "ncs.find_automatically=false".

Example:

phenix.refine model.pdb data.mtz ncs.txt main.ncs=true
ncs.find_automatically=false

I'm sure you can do this from phenix.refine GUI as well.

Cheers,
Pavel.

On 3/2/09 5:46 PM, Van Den Berg, Bert wrote:
>
> 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
>
>
>

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

Previous message:
Subject: PhD Studentships at Cardiff Medical School
From: Pierre Rizkallah rizkallahp {- at -} CARDIFF {- dot -} AC {- dot -} UK
Date: 2009-03-03

Next message:
Subject: PhD Opportunities in Structural Biology
From: Wojciech Rypniewski wojtekr {- at -} IBCH {- dot -} POZNAN {- dot -} PL
Date: 2009-03-03