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[ccp4bb] Antw: Re: [ccp4bb] R/Rfree values

Dear Rohit Additionally to the very good suggestions, I'd feed the structure into the PDB_REDO server. Its a fast and easy way to detect if the refinement strategy is correct. The server gives you a good feeling how tight the x-ray weights need to be. If however PDB_REDO does not manage to

Re: [ccp4bb] R/Rfree values

Hi Rohit, Along with many excellent suggestions you already got...I want to add the possibility of the presence of twining (even a small but significant percent) and/or the presence of t-NCS in the data. Good luck! Sudipta. On Wed, Dec 14, 2016 at 12:19 PM, Prem Prakash

Re: [ccp4bb] R/Rfree values

Dear Rohit, I am totally agree with Mark, that just R free and R work does not decide the structure solved, you have to see other parameters as Mark already suggested. What is and redundancy and also what is the mosaicity? please look at these parameters too. Best Prem On Wed, Dec 14, 2016 at

Re: [ccp4bb] Message from the Uppsala EDS: "Morituri te salutant"

The replacement of the EDS might be an excellent opportunity to upgrade/include the newer EDSTATS metrics and make these raw data also downloadable/parse-able for analysis purposes (xml). A server option where you can send in your own PDB files (included in the validation server?) before

Re: [ccp4bb] Bug in latest COOT

Same with me, I have Mac OS 10.11.6 (El CApitan). I couldn’t add terminal residues, then went three CCP4 updates back, it got OK, but I still can’t add OXT. Olga > On 14 Dec 2016, at 04:51, Jobichen Chacko wrote: > > Dear All, > Any solution to this problem. > I am also

[ccp4bb] 2016 Remediation of 3DEM Entries in the PDB archive

The wwPDB and the EMDataBank/Unified Data Resource for 3DEM Project have collaborated to update the experimental methods descriptions of all electron microscopy and electron crystallography-derived structures in the PDB archive. With this work now

Re: [ccp4bb] R/Rfree values

Dear Rohit, Look at what percentage of the reflections are in the Rfree set, if its less say 5 %; and you have a good redundancy you can use 10 %. You might like to use the other Rfree set[1 if you have already used the 0 set] or consider using the whole set of reflections as a free set if need

Re: [ccp4bb] Why aren't green reflections on Mosflm integrated?

Walt is correct, the denzo/HKL2000 is an exception. It integrates all reflections that cross the Evald sphere, due to having special treatment of reflections with large Lorentz correction. It works fine in normal cases, even with somewhat misaligned rotation axis. These reflections are

Re: [ccp4bb] R/Rfree values

In addition to what others have mentioned, you might want to consider the unpleasant possibility that part of your structure is simply built incorrectly. Sometimes rebuilding a short loop or even a few residues in that loop can do the trick. Look carefully for regions of your map with poor

Re: [ccp4bb] R/Rfree values

es - look carefully at your data quality indicators - batch scales, Wilson plot - moments etc.. tHese can show up if there is a problem with ice rings or crystal decay or whatever. Then I always look at the REFMAC plot of v If they overlap well - good - but problems with scaling will show up

Re: [ccp4bb] Message from the Uppsala EDS: "Morituri te salutant"

Thank you Uppsala lot - it has been a great service and taught a lot of people that "The map is the Message" Eleanor Dodson On 14 December 2016 at 12:54, Daniel Picot wrote: > Veni vidi > I wil have to change my advices and lectures: go and look at the Uppsala > Electron

Re: [ccp4bb] R/Rfree values

Dear Rohit, I wouldn’t judge a structure just by the Rwork and Rfree values, but also by the validation and other statistics (bond lengths, angles, Ramachandran plot, map quality, fit to map, average B values). If these are all ok, you should be able to “get away with” an Rfree of 33%. In your

Re: [ccp4bb] R/Rfree values

Dear Rohit, Try to run sfcheck or XTRIAGE and check, if your data is fine. Check for twinning or pseudo-translation. You can send your processed mtz to me and I would be more than happy to help you. You can look into cumulative intensity distribution (if you processed with XDS, it will be in

[ccp4bb] R/Rfree values

Dear All, I am solving a data of 2.5 A (C121 space group). Right now the R/Rfree values are 26/33, after many cycles of refinements (With or With out water) the R/Rfree values still same. Zanuda suggests that the space group seems to be correct and the model is looking fine in coot. Some one

Re: [ccp4bb] Message from the Uppsala EDS: "Morituri te salutant"

Veni vidi I wil have to change my advices and lectures: go and look at the Uppsala Electron Density Server EDS It has been extremely useful. Even sometimes vici Daniel Le 13/12/2016 à 19:52, Patrick Loll a écrit : Ave atque vale. The EDS was hugely useful (and will continue to be so in its

Re: [ccp4bb] Why aren't green reflections on Mosflm integrated?

Dear Walt, As Tim has said, this is indeed related to the Lorentz correction. These reflections have a large Lorentz correction which is also very sensitive to the crystal orientation, so any small error in orientation can result in a big change to the Lorentz correction and

Re: [ccp4bb] Why aren't green reflections on Mosflm integrated?

Hi Looking at this in a slightly different way: The Lorentz factor is inversely related to the speed at which the reciprocal lattice points traverse the Ewald sphere; those reflections close to the rotation axis have a speed through the Ewald sphere that is tending towards zero (because they

Re: [ccp4bb] Why aren't green reflections on Mosflm integrated?

Dear Walt, reflections close to the rotation axis stay in reflecting condition for a long time, where time is sensibly measured in degrees. Their intensities cannot be determined reliably, and I would think that most integrating programs, including HKL2000, reject such reflections. Best

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