Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

Hi Gerard, > On 22 Feb 2021, at 19:38, Gerard Bricogne wrote: > > Did you perhaps deposit only part of the data you collected for the > remote wavelength? For example, only one of several orientations that you > might have collected in order to try and fill the cusp? data_r2xgfsf in the

Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

Hi Gerard, fortunately I still have the data for this structure on my computer - and not on tape or somesuch. Below is the summary of the SCALA logfile, from which the statistics were quoted. Collection was a single sweep of 180 degrees. I'll send you privately the complete log file and the

Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

Dear Patrick, Mark and colleagues, Examining the data associated to PDB entry 2XGF using the PDBpeep server, i.e. at http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=2xgf shows a large region (marked up in dark blue) of missing measurements where the analysis of the trends

[ccp4bb] Celebrate PDB50 at the Inaugural May 4-5 Event (register by March 15)

Throughout 2021, the wwPDB will be celebrating the 50th anniversary of the PDB archive (http://wwpdb.org/pdb50). The inaugural symposium will be held virtually on May 4-5, 2021. The online sessions will take place between 11 a.m. – 4:30 p.m. ET each day. The event will be recorded and made

[ccp4bb] Structural biology postdoc position in Denmark

We have a 3 year postdoc position available in the group studying structural and functional aspects of receptors and signalling components important for plant-microbe interactions. We recently obtained structures of a symbiotic receptor (Bozsoki, Science 2020) and a surveillance receptor (Wong,

Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

Hi Patrick, couldn't see any text in you email, just the subject and the picture, but 2XGF is our T4 long tail fibre tail tip structure from 2010. (2XGF stands for "2nd eXtraordinary Great Fibre", at least that's what I *modestly* imagine..). I think it's probably one or more of: - noise (was

Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

Depending upon the amount of radiation exposure, the iron might be reduced (or more likely, in a mixed oxidation state) by the X-ray beam. Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical

Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

Sorry, in my previous email I was oblivious to the fact that there was Fe. Iron is almost certainly oxidized. So, if you started collecting data with reduced iron, but it got oxidized during data collection, you are probably using the parametrization for the reduced rather than oxidized one in the

Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

Is the oxidation state of the coordinated atom, or the identity of that atom correct? If there was a very slightly bigger atom, it would take care of the positive residual density and would push out the His side chains a little bit, which in turn could take care of the negative ones. Or, the same

Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

Hi, as others pointed out electron rich elements tend to amplify imperfections visible in Fo-Fc maps. Consider: - refining occupancy of Fe, the site may be partially occupied; - refining f' and f'' if data are anomalous; - surrounding histidines may 'see' this Fe as a nonbonded interaction and

Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

Hello, there usually is noise in the difference map near electron-dense elements. Maybe refining against I(+) and I(-) might help, as someone suggested a few months ago or perhaps you have already done that. It would be interesting to know if it helps. Cheers, Jon.C. Sent from ProtonMail

[ccp4bb] Virtual Annual CCP4/APS Crystallographic School (2021) in the US

Dear Colleagues, We are pleased to announce the virtual annual CCP4/APS crystallographic school "From data collection to structure refinement and beyond" will be held on June 14-25, 2021 at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All

Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

Well - that doesnt look too bad - it is hard to see in a screenshot but presumably the N & C in the ring are correctly placed? Why is there positive density over the Fe? Are there other similar features elsewhere in the map which can be assigned to noise? Eleanor On Mon, 22 Feb 2021 at 15:27,

[ccp4bb] synthetic protein materials postdoc position available - deadline 2 March

Dear all, We have a postdoc position available to work on a synthetic protein materials project in collaboration with Prof. Milo Shaffer (Dept of Materials) and industrial partners. https://www.imperial.ac.uk/jobs/description/MED02267/research-associate-synthetic-protein-materials

[ccp4bb] Post-Doctoral position in Porto, Portugal

We are looking for a highly motivated post-doc to join the Macromolecular Structure group of i3S - Instituto de Investigação e Inovação em Saúde (https://www.i3s.up.pt/research-group?x=113) in Porto, Portugal. The position, funded for 3 years, is expected to start in April 2021. Building

Re: [ccp4bb] Linux Distro for setting up workstations - Is CentOS still a good choice?

Dear Tom, I updated the workstation with Ubuntu 16.04->20.04 This update broke 3d vision and I am thinking about moving back to Ubuntu 16.04. Other programs work well. вс, 21 февр. 2021 г. в 10:59, Folmer Fredslund : > Dear Tom > > Be aware that python2 is currently not supported. It is