Re: [ccp4bb] CCP4BB Digest - 12 Feb 2009 to 13 Feb 2009 (#2009-45)

Hi Ho, this might be helpful: R.J. Read, Acta Cryst. (1999). D55, 1759-1764 "Detecting outliers in non-redundant diffraction data". Pavel. On 2/13/2009 4:45 PM, Ho-Leung Ng wrote: Hi Clemens, Can you elaborate on the effects of improper inclusion of low resolution (bogus?) reflections?

Re: [ccp4bb] CCP4BB Digest - 12 Feb 2009 to 13 Feb 2009 (#2009-45)

Hi Clemens, Can you elaborate on the effects of improper inclusion of low resolution (bogus?) reflections? Other than rejecting spots from obvious artifacts, it bothers me to discard data. But I can also see how a few inaccurate, very high intensity spots can throw off scaling. ho UC Berkel

Re: [ccp4bb] unstable refinement

Hi John, Just to play devils advocate (is that the right terminology?), a random list of potential issues that could cause that .. seen that, been there, suffered ... * Rfactor tells you something about your X-ray term, so if you have the weight on the X-ray term too low (or the weight on geome

Re: [ccp4bb] unstable refinement

Dear John, If by unstable refinement you mean a significant increase of Rfactors during refinement, then there is a problem in the software you use and the best thing you can do is to notify the developers of that software so they can fix the problem. I can't tell for other software, but I'

Re: [ccp4bb] unstable refinement

John, I would argue with the statement that a steadily increasing Rfree denotes an unstable refinement. This could be due to the fact that your initial model is biased by information not in your data. This would include previous refinement against the TEST set, use of a high resolution MR model

Re: [ccp4bb] Refinement: Basic questions

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On Fri, 13 Feb 2009, Andy Millston wrote: I have some very basic questions about model refinement process. 1. Why Refmac5 refinement from Coot GUI gives different results than Refmac5 refinement from CCP4i? One obvious difference is that COOT ref

[ccp4bb] Refinement: Basic questions

I have some very basic questions about model refinement process. 1. Why Refmac5 refinement from Coot GUI gives different results than Refmac5 refinement from CCP4i? One obvious difference is that COOT refinements are local whereas CCP4i refinements are global. But why should it make a major dif

[ccp4bb] Announcement: TotalCryst school in Grenoble, April 1 -3, 2009

TotalCryst is a universal methodology for crystallographic structure solution and refinements of arbitrary polycrystals and powders. The method determines the molecular arrangement within each grain. It applies to simple inorganic structures as well as to large macromolecules and it attempts to

[ccp4bb] Beamtime at SLS X06SA - deadline: 15th Feb

= SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE UNDULATOR BEAMLINE X06SA AT SLS FROM MAY TO AUGUST 2008 = - PILATUS 6M pixel detector available for us

[ccp4bb] unstable refinement

Hi, I would like to survey the group for causes and potential solutions to unstable refinement (the steady and upward drift of R and Rfree in each cycle of refinement). I am currently aware of the following potential causes: twinning (meohedral, pseduomerohedral, or epitaxial), anisotropy, pseud

Re: [ccp4bb] native gel

Dear Jothi, Here is an alternative. Selection of membrane protein targets for crystallization using PFO-PAGE electrophoresis. Cleverley RM, S