Thanks Ian, I'll keep posting :) Brigitte
---- Original message ---- >Date: Tue, 4 Oct 2011 21:19:40 +0100 >From: Ian Tickle <ianj...@gmail.com> >Subject: Re: [ccp4bb] Calculate real-space R-factor/corr coeff for ligand >To: bkziervo...@uchicago.edu >Cc: Adam Ralph <adam.ra...@maths.nuim.ie>, CCP4 bulletin board ><CCP4BB@jiscmail.ac.uk> > > On Tue, Oct 4, 2011 at 7:14 PM, > <bkziervo...@uchicago.edu> 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
