Thanks Ian, I'll keep posting :)
Brigitte
---- Original message ----
>Date: Tue, 4 Oct 2011 21:19:40 +0100
>From: Ian Tickle <[log in to unmask]>
>Subject: Re: [ccp4bb] Calculate real-space R-factor/corr coeff for ligand
>To: [log in to unmask]
>Cc: Adam Ralph <[log in to unmask]>, CCP4 bulletin board <[log in to unmask]>
>
> On Tue, Oct 4, 2011 at 7:14 PM,
> <[log in to unmask]> wrote:
>
> Hi Adam and Ian,
>
> Thanks for your help. If I re-calculate the
> R-factors with the correct absolute values I get
> more reasonable values. However, I'm still a bit
> confused because the output given by the
> Overlapmap program is structure factor values,
> which are used to calculate the real-space
> R-factors. Should this not be Rho values
> instead? Additionally, a lot of my structure
> factors, even for the protein, which I know fits
> well within the experimental density, are 0 for
> the sidechains or negative. Any idea what's
> going on here? I've attached some sample data
> from the Overlapmap output file. Thanks in
> advance.
>
> Brigitte
>
> Hi Brigitte
>
> Yes I agree with you that the output is very
> confusing! I don't know exactly what 'Fobs' &
> 'Fcalc' are but I'm pretty sure they can't be
> structure factors. I would guess that 'F' is
> actually rho (i.e. rho calculated by FFT from F).
> According to the man page overlapmap only inputs &
> outputs maps: nowhere does it mention reading or
> writing SFs. Very confusing!
>
> Also why the values are small or negative, I've no
> idea as I've never used overlapmap. I would keep
> posting to the BB in the hope that someone can solve
> your problem.
>
> Cheers
>
> -- Ian
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