| Quick navigation: | Home | Site Map || References | Biography || Copyright | Other copyright | Contact us | Advert | | |
Re: [ccp4bb] DANO from PDB |
||
- Protein crystallographyMain steps:- Protein purification- Crystallisation Special:- Programs for crystallography- X-ray detectors Basic tutorials:- Chemistry- Protein - Peptide - Amino Acids Xtal community:- CCP4BB |
CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: DANO from PDB From: Bart Hazes bart {- dot -} hazes {- at -} UALBERTA {- dot -} CA Date: 2007-06-13 Eleanor Dodson wrote: > Well - the old way to estimate sigma was Sqrt(I**2 + > constant_representing background) and then get > Sigma_F as ~ sqrt(SigI)/(2*F ) . > sftools would calculate that for you and append it to the output file.. > Eleanor I suggested something similar to Pete but sufficiently different that I'd like to post it. I expect that in the example above I**2 should be F**2 otherwise SigI is proportional to I when I >> background rather than proportional to Sqrt(I) as expected for pure counting statistics. Bart For any purist there is no good way. If you look for something that you can explain concisely in a methods section and that has at least some logic to it you could convert your Fcalc to intensities (F**2). Multiply this by a conversion factor C with C being four divided by the average intensity at the highest resolution of the data set (4/ square root of this as your SigmaI. The idea here is to convert the calculated intensity to photon counts recorded in the experiment. A "typical" data set has about I/SigI of 2 at the high resolution. Since SigI is the square root of I if it is solely dependent on counting statistics, setting C to give an average I of 4 in the highest resolution shell should give an I/SigI of about two after you set SigI to the square root of I. I don't actually expect that this will closely mimic an experimental I/SigI versus resolution pattern but it should be easy to calculate with sftools so you can go ahead and give it a try. Bart > > Eleanor Peter Adrian Meyer wrote: > >>> I add a fake "sigma" column for each "data" column because so many >>> >> >> programs require one. >> >> This is slightly tangential, but does anyone know of a good way to >> generate semi-realistic sigma values for calculated/simulated data? >> >> The best I've been able to do is borrow from an experimental dataset of >> the same protein (after scaling), but that doesn't work unless you've got >> an experimental dataset corresponding to your simulated one. I also >> tried >> a least-squares fit (following a reference I don't have in front of >> me...this was a while ago), which didn't result in a good fit for our >> data. >> >> Pete >> >> Pete Meyer >> Fu Lab >> BMCB grad student >> Cornell University >> >> >> > > > -- ============================================================================== Bart Hazes (Assistant Professor) Dept. of Medical Microbiology & Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax: 1-780-492-7521 ============================================================================== CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
|
| ProteinCrystallography.org: Copyright 2006-2010 by Quid United Ltd |