[ccp4bb] Validation Question

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2008 <-- May 2008 <-- 12 May 2008

Previous message:
Subject: Re: phasing at low resolution
From: Raja Dey deyraja1 {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2008-05-09

Next message:
Subject: Re: Validation Question
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2008-05-12

Subject: Validation Question
From: Simon Kolstoe s {- dot -} kolstoe {- at -} UCL {- dot -} AC {- dot -} UK
Date: 2008-05-12

Dear ccp4bb,

I have heard from many people that molprobity is the gold standard as
far as validation is concerned. As I am just about to deposit a
structure I therefore figured it was best to use molprobity in guiding
the final stages of my refinement. I do not have enough data to
justify adding hydrogens in my refinement, however as molprobity
suggests adding hydrogens for validation purposes I obediently did so
and (surprise surprise) found that I had a number of clashes
(clashcore 17.6). Just as an experiment I re-ran refmac including
hydrogens and this time my clash score was much lower and apparently
acceptable (6.27), whilst my R factors were pretty much identical to
before. So my question is this - do I ignore the normal obs:params
calculation and just refine my structure with hydrogens (resolution
1.9, 99.9% complete) as according to molprobity this gives me a
"better" structure, or do I just ignore the clashscore targets in
molprobity based upon not having enough data to justify refining this
component?

Thanks,

Simon

CCP4bb navigation

CCP4bb <-- 2008 <-- May 2008 <-- 12 May 2008

Previous message:
Subject: Re: phasing at low resolution
From: Raja Dey deyraja1 {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2008-05-09

Next message:
Subject: Re: Validation Question
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2008-05-12