Re: [ccp4bb] methews coefficient and validation of 60mer

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

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

Previous message:
Subject: Re: Refining residues as rigid bodies
From: Frederic VELLIEUX frederic {- dot -} vellieux {- at -} ORANGE {- dot -} FR
Date: 2009-12-02

Next message:
Subject: Re: decrease of background with distance?
From: John R Helliwell jrhelliwell {- at -} GMAIL {- dot -} COM
Date: 2009-12-02

Subject: Re: methews coefficient and validation of 60mer
From: Martyn Winn martyn {- dot -} winn {- at -} STFC {- dot -} AC {- dot -} UK
Date: 2009-12-02

Yes, matthews_coef has a limit of 48. You need to change:
PARAMETER (MAXMOL=48)
in $CPROG/matthews_coef.f and recompile. Ask if you need help with
this.
So looks like its time to increase the parameter in line with the
capabilities of computers and crystallographers ....
BTW matthews won't tell you 60, it will tell you somewhere between 40
and 80. Also I assume this is protein - I have fixed the matthews task
recently for RNA/DNA.

The CCP4 Procheck Ramachandran is deprecated, since it is based on old
angle distributions. Try Rampage, e.g. via the ccp4i -> Validation &
Deposition -> Validate Model and/or Data task.

Cheers
Martyn

On Wed, 2009-12-02 at 12:57 +0530, Pankaj Chauhan wrote:
> Hi ,
> In one of my 60mer structure at 3.5 A, , when I run methews in ccp4i,
> it doesn't show number of molecules in asymmetry above 40, is there
> any other program which can show all the molecules in assymetric unit.
> Second problem, for validation of 60mer, i was willing to use
> Procheck which gives residues in allowed region, additional allowed
> region, generously allowed region and disallowed region in
> ramachandran plot. But procheck is not giving any output here in
> 60mer. Although i could validate the structure using coot and phenix,
> but they dont give residues in generously allowed region.
> KIndly give some suggestion and help,
> Regards,
>
> --
> Pankaj Chauhan
> Senior Research Fellow, PhD Scholar
> Crystallography Laboratory
> Division of Protein Science & Engg.
> IMTECH , Chandigarh, INDIA
--
***********************************************************************
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455 E-mail: martyn.winn@stfc.ac.uk *
* Fax: +44 1925 603825 Skype name: martyn.winn *
* URL: http://www.ccp4.ac.uk/martyn/ *
***********************************************************************

CCP4bb navigation

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

Previous message:
Subject: Re: Refining residues as rigid bodies
From: Frederic VELLIEUX frederic {- dot -} vellieux {- at -} ORANGE {- dot -} FR
Date: 2009-12-02

Next message:
Subject: Re: decrease of background with distance?
From: John R Helliwell jrhelliwell {- at -} GMAIL {- dot -} COM
Date: 2009-12-02