[ccp4bb] Updated SAUC Cell Database

2017-12-29 Thread Herbert J. Bernstein
The SAUC Cell Database has been updated to 122596 PDB cells and 397452 COD cells. SAUC is accessible at http://iterate.sourceforge.net/sauc or http://flops.arcib.org:8084/sauc/ The second link is to a faster machine, but with less network bandwidth If you would like to install your

Re: [ccp4bb] Asp-Asp pair facing each other at <3.0 A distance

2017-12-29 Thread Goldman, Adrian
All true, I did my undergraduate thesis (at cambridge about 10**6 years ago it feels) on the formation of carboxylate-pairs in the gas phase…. But I agree with the thread: there is a metal there; it’s almost certainly not Mg, but it’s hard to say without further data whether its Mn, Fe, Cu, Zn

Re: [ccp4bb] how to improve the diffraction quality of the crystals and avoid icerings

2017-12-29 Thread Doug Juers
Hi Yuvraj, Here are some thoughts in addition to what's been suggested already: 1. A good recent reference is here: http://journals.iucr.org/f/issues/2015/06/00/en5564/index.html 2. The image you sent suggests cubic ice, indicating a higher glycerol concentration (maybe 35 or 40%) is needed.

[ccp4bb] Les Houches/TSRC Workshop on Protein Dynamics, Chamonix Valley, May 27-June 1, 2018

2017-12-29 Thread martin weik
Dear colleague, Registration is open for the Les Houches/TSRC Workshop on Protein Dynamics, to be held in Les Houches, close to Chamonix at the heart of the French Alps, from May 27 to June 1, 2018. This international workshop is a forum for presenting and discussing results from

Re: [ccp4bb] Asp-Asp pair facing each other at <3.0 A distance

2017-12-29 Thread Tristan Croll
In this case, yes - there’s clearly a metal ion coordinated there. But for the record, it is entirely possible (if somewhat rare) to get acidic side chains directly contacting each other. Look up “carboxyl-carboxylate pair”. They’re typically found at low pH and/or in quite protected

Re: [ccp4bb] how to improve the diffraction quality of the crystals and avoid icerings

2017-12-29 Thread Kay Diederichs
Hi Yuvaraj, the importance of proper cryo mounting is under-appreciated in the community. Intensities of reflections on or close to ice rings cannot be recovered by the data processing software with good accuracy, which is detrimental for structure solution and refinement. Thus it is vital to

Re: [ccp4bb] Fwd: [ccp4bb] how to improve the diffraction quality of the crystals and avoid icerings

2017-12-29 Thread Eugene Osipov
Hi, Yuvraj, I can suggest two methods: 1) collect a dataset at room temperature 2) crystallize your protein in cryoconditions. That is add 25 % of glycerol to your crystallization conditions and perform small optimization in terms of precipitant concentration. 2017-12-29 7:55 GMT+03:00 Prem