Re: [ccp4bb] XDS questions

Hi, I do this by editor (and cut / paste). Clumsy but works. Let me know if you find a more elegant way. Cheers, Boaz Original message From: Wei Wang Date: 21/11/2016 19:05 (GMT+02:00) To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] XDS questions

[ccp4bb] Inclusion Bodies

We have been expressing a family of human proteins as inclusion bodies in E. coli, which we can be refolded and crystallized. However, three members show no expression either as inclusion bodies or as soluble proteins. The genes were ligated into the pE21d vector with either a His-tag or no

Re: [ccp4bb] Inclusion Bodies

Hi, Well, sometimes proteins don't express even though they are from the same family and their "cousin" behaved very well. I found the followings helpful: 1. forget about the concept "this special strain *should* work because it is a Rosseta/ pLysS etc." Sometimes it's a long mRNA, sometimes a

[ccp4bb] local coordinate uncertainty / SFCHECK questions

Hi All, We have recently solved several structures of a membrane protein in slightly different conformations at low resolutions (3.9-4.2 A). We would like to see that these structures reflect truly different conformations and to what extent these structures are discernible. To answer this

Re: [ccp4bb] local coordinate uncertainty / SFCHECK questions

On Monday, 21 November 2016 11:53:22 PM Seok-Yong Lee wrote: > Hi All, > > We have recently solved several structures of a membrane protein in slightly > different conformations at low resolutions (3.9-4.2 A). We would like to see > that these structures reflect truly different conformations

[ccp4bb] Cryo-EM in Australia: group-leader and staff-scientist positions

Dear cryo-EM community, Two continuing, full time positions are available at the University of Wollongong in Australia: Staff Scientist (Cryo-Electron Microscopy): http://uow.employment.com.au/jobs/Staff-Scientist--Cryo-Electron-Microscopy-/2487 Senior Lecturer / Associate Professor

Re: [ccp4bb] XDS questions

Dear All, I agree with Tim - what I was getting at was to perform the scaling exactly once - i.e. with AIMLESS or XDS CORRECT but not both The behaviour Tim describes below is exactly what xia2 does :) Best wishes Graeme -Original Message- From: CCP4 bulletin board

Re: [ccp4bb] XDS questions

Dear All, Just to understand more, the XDS_ASCII.HKL file generated after running XDS contains scaled and merged reflections? Moreover, what happens exactly, if you use XDS_ASCII.HKL file in AIMLESS instead of INTEGRATE.HKL file?? I ran AIMLESS separately, one using already scaled XDS_ASCII.HKL

Re: [ccp4bb] XDS questions

Dear Nishant, XDS_ASCII.HKL contains corrected, scaled, but not merged reflections. You can specifically ask XDS to merge your data, but I would not do so unless really necessary - you loose a lot of information. I would like to offer a different opinion to Graeme's: You can read XDS_ASCII.HKL

Re: [ccp4bb] XDS questions

Dear Nishant Your statistics will be better taking XDS_ASCII because the scaling has been performed twice i.e. you have had two goes (with different models) of reducing the differences between reflections. This will *always* make the R factors etc smaller – whether the data are better or more

Re: [ccp4bb] XDS questions

XDS-CORRECT and Aimless use 1. different scaling models - CORRECT includes a poorly documented correction across the detector plane not present in Aimless: this may or may not be a Good Thing 2. different outlier rejection algorithms - XDS seems to reject more observations 3. different

[ccp4bb] facility manager position X-ray crystallography and biophysics

** X-ray crystallography and biophysics facility manager ** The Max Planck Institute of Molecular Physiology, Dortmund, Germany, is looking for a X-ray crystallography and biophysics facility manager. The ideal candidate for this position should have a PhD degree in macromolecular

Re: [ccp4bb] XDS questions

My personal test shows that the different paths vary little with each other, as long as the scaling is done only once. Another way could be what is said on XDSwiki: Minimum I/Sigma=50, CORRECTIONS=MODULATION, NBATCH=1. Then the XDS_ASCII.HKL is handed over to Aimless with default settings. One