Quick navigation:        Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |   
Protein structure
 

Re: [ccp4bb] XDS and overlaps
 

Basic tutorials: 		 
 

CCP4bb navigation

CCP4bb <-- 2008 <-- February 2008 <-- 22 February 2008
Previous message:
Subject: Re: cns and refmac refinement
From: Chavas Leo ccp4hnaalas {- at -} GMAIL {- dot -} COM
Date: 2008-02-21 		Next message:
Subject: Re: XDS and overlaps
From: Petri Kursula pkursula {- at -} SUN3 {- dot -} OULU {- dot -} FI
Date: 2008-02-22


Subject: Re: XDS and overlaps
From: Martin Hallberg Martin {- dot -} Hallberg {- at -} KI {- dot -} SE
Date: 2008-02-22
There is of course nothing stopping you from having both severe
overlap problems and twinning :-(

> In this case, XDS-processed data is clearly twinned, if one were to
> believe moments and the cumulative intensity distribution calculated
> by truncate (and everyone should - channelling Dr. Dodson).
>
> Why I'm worried about XDS separating relatively overlapped spots is
> the funny intensity stats that may result from this (as George
> Sheldrick and Martin Hallberg has pointed out)? The incomplete
> HKL2000-processed data (70%) still has intermediate values for the
> intensity stats, leaning towards twinning. This somewhat agrees with
> twinning, but not overzealous data integration.

What happens if you play with spot parameters (to increase the number
of reflections identified as overlaps) in Denzo? This will reduce the
completeness even more but might be a worthwhile exercise to figure
out what the problem really is. Can you get cleaner intensity
statistics this way?
Similarly, you can play with the MINPK parameter in XDS (as suggested
by Kay).

Best regards,

Martin

.
B. Martin Hallberg, PhD
Assistant professor
Department of Cell and Molecular Biology
Medical Nobel Institute
Karolinska Institutet
Nobels v. 3
SE-171 77 Stockholm
Sweden

CCP4bb navigation

CCP4bb <-- 2008 <-- February 2008 <-- 22 February 2008
Previous message:
Subject: Re: cns and refmac refinement
From: Chavas Leo ccp4hnaalas {- at -} GMAIL {- dot -} COM
Date: 2008-02-21 		Next message:
Subject: Re: XDS and overlaps
From: Petri Kursula pkursula {- at -} SUN3 {- dot -} OULU {- dot -} FI
Date: 2008-02-22


ProteinCrystallography.org: Copyright 2006-2007 by Quid United Ltd