Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

Its not just the Ramachandran outliers - the attached metrics summary courtesy of the PDB raises a lot of questions about the accuracy of this structure As for Nature being right, it was an attempt at humor. Dear crystallographers, The PDB entry

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

It was published in Nature so it must be right :) ... Dear crystallographers, The PDB entry http://www.rcsb.org/pdb/explore.do?structureId=3BDN has 16.5% Ramachandran outliers. When I opened this PDB file in coot and checked for Ramacha

[ccp4bb] DSSP and PDB secondary structure assignments

I've recently noticed that the Helix and Sheet records in PDB entries differ from those generated by DSSP and would like to ask if anyone can explain how the PDB makes the assignments. Until now I'd always assumed that the PDB and DSSP records were the same. As an example I've listed a few lin

[ccp4bb] Postdoctoral Fellowship in Membrane Protein Structural Biology at NIH

Structural studies on glutamate receptor ion channels: A postdoctoral position in X-ray crystallography is available immediately in the group of Dr. Mark L. Mayer, in the Laboratory of Cellular and Molecular Neurophysiology at the NIH in Bethesda MD, USA. This opening is part of an established

[ccp4bb] UV microscopes for Xtal visualization

I have read the paper by Gill in Acta Crys F66: 364-372 and wonder what other peoples experience has been with the MUVIS from Formulatrix and the JANsci microscope for imaging 96 well plates. The JANsci instrument seems to have an advantage over the MUVIS in having two objectives. For detec

[ccp4bb] Deposition of riding H: R-factor is overrated

Huh? That's not a cif fragment. What file are you looking at? In my experience the PDB feeds back to you a cif format structure factor file with a name like rcsb054058-sf.cif Near the top of that file you should find a description of the data columns. The columns present depend on what you fed

Re: [ccp4bb] Deposition of riding H: R-factor is overrated

Ethan wrote I believe that deposition of Fc Phic FOM should be required. Certainly it should be the recommended practice. For the same series of structures I just deposited, which started the the riding H discussion, my mtz file had Fc Phic FOM + other data put out by Phenix - pavel can ela

Re: [ccp4bb] Deposition of riding H

However this thread appears to have reached the point where not much new ground is being broken. As the person who started this thread I'll second Phil Jeffrey's comment. I chose to continue my depositions with riding H, and the rcsb agreed to accept the coordinates. Its been great hearing the

[ccp4bb] Deposition of riding H

Here's one for the community, which I'll post to both Phenix and CCP4 BBs. Where does the crystallographic community stand on deposition of coordinates with riding hydrogens? Explicit H are required for calculating all atom clash scores with Molprobity, and their use frequently gives better g

[ccp4bb] how to improve Rfree?

You can also pick thin shells with SFCHECK and with 12-fold NCS the referees will likely not be kind if you dont!!! -- Mark

[ccp4bb] Postdoc positions available NIH Jan 2010

Postdoctoral positions are available to study the structure and function of neurotransmitter receptors in a group at the NIH main campus, Bethesda, MD 20892 We are looking for highly motivated young scientists who would like to join a group which combines crystallographic studies with bioch

[ccp4bb] Slightly off-topic - silica based columns

Slightly off-topic - but these days most crystallographers are interested in protein purification. What experience do people have with silica based columns for size exclusion chromatography. We are interested in resolution, stability, column life time, and ease of cleaning column compared to