Simon,
You should always include H atoms in refinement whatever the resolution,
I can't think of any reason for not doing so. They are not refined
independently but 'ride' on the parent atom, so don't contribute to the
parameter and restraint counts, and as you say it is essential that they
are included when running Molprobity, you won't get sensible results
without them.
-- Ian
> -----Original Message-----
> From: [log in to unmask]
> [mailto:[log in to unmask]] On Behalf Of Simon Kolstoe
> Sent: 12 May 2008 12:08
> To: [log in to unmask]
> Subject: Validation Question
>
> 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
>
>
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