[ccp4bb] An opening for a post-doctoral position at NIMHANS, Bangalore, India

2014-12-03 Thread Padmanabhan B
*Applications are invited for a post-doctoral position at NIMHANS, Bangalore, India.* At National Institute of Mental Health and Neuro Sciences (NIMANS), a post-doctoral / Research Associate position is available in our Structural Biology Lab. The candidate should have a Ph. D with substantial re

[ccp4bb] tRNA and aminoacyl-tRNA synethetase complex question

2014-12-03 Thread Hank
Dear CCP4BB Members, I'm trying to design a tRNA expression system for its co-crystal structure with an aminoacyl-tRNA synthetase (class Ia, eukaryotic). My question is how a specific tRNA is chosen among tRNAs of various anticodons for co-crystallization attempts. Can codon usage be a basis of th

Re: [ccp4bb] Intensities and amplitudes

2014-12-03 Thread Boaz Shaanan
Hi Randy, Question regarding your reply to Pavel: >That may well involve the French & Wilson algorithm, but can take advantage of >whatever is understood by the program (e.g. anisotropy and >translational >non-crystallographic symmetry, both of which in principle can be modeled >better as the

[ccp4bb] off-topic: short oligo concentrator

2014-12-03 Thread Xiao Xiao
Hi all, We're planning to use short oligos to co-crystallize with protein. Basically we will synthesis that from company and then purified by ion-exchange then concentrate it. Does any one know a easy way or product to concentrating short oligo (such as 5nt)? The only way came to my mind, is to de

Re: [ccp4bb] HKL2000 Display

2014-12-03 Thread Muhammed bashir Khan
Hi All; Thanks everybody. It was wrong detector site file. Now its working. Thanks Bashir On Wed, December 3, 2014 17:19, David Schuller wrote: > Yes, it is probably the wrong detector type, or the wrong parameters, > perhaps binned vs. unbinned. > > > On 12/03/14 07:25, David Waterman wrote: >

Re: [ccp4bb] Intensities and amplitudes

2014-12-03 Thread Randy Read
Dear George, Yes, we’ve developed new likelihood functions that work with intensity data. They’re already available for the molecular replacement calculations in recent nightly-build versions of Phaser (though it’s been a while since a new nightly was released, and we’ve fixed a few problems w

Re: [ccp4bb] HKL2000 Display

2014-12-03 Thread Dominika Borek
You are using an incorrect site file. Whatever you provided to the program as description of the detector used during data collection needs to be changed. D. Muhammed bashir Khan wrote: > Hi All; > Could somebody explain why my Display image in HKL2000 look like that. Image attached. > Thanks for

Re: [ccp4bb] HKL2000 Display

2014-12-03 Thread David Schuller
Yes, it is probably the wrong detector type, or the wrong parameters, perhaps binned vs. unbinned. On 12/03/14 07:25, David Waterman wrote: Hi Muhammed, It looks a lot to me like denzo thinks your detector has a larger image size than the actual number of elements in the array. However, I d

Re: [ccp4bb] HKL2000 Display

2014-12-03 Thread Hattne, Johan
I’ve seen this when the description in the site file does not actually match the data. // Johan On Dec 3, 2014, at 7:25, David Waterman wrote: > Hi Muhammed, > > It looks a lot to me like denzo thinks your detector has a larger image size > than the actual number of elements in the array. Ho

Re: [ccp4bb] Intensities and amplitudes

2014-12-03 Thread George M. Sheldrick
Dear Randy, I could not agree more. Statistical methods for phasing and refinement must be better using the observed intensities and their esds than with (c)truncated F-values. In particular one should merge intensities, not truncated Fs! To elaborate on Harry's comment, when SHELXL started refin

[ccp4bb] Reminder: Open postdoc positions in research and scientific software development (EMBL Hamburg, Lamzin)

2014-12-03 Thread Philipp Heuser
Just a reminder: The deadline for applications is 7 December 2014. Next Sunday! Philipp Dear colleagues, I would like to make you aware of two open positions in the Lamzin group at the EMBL in Hamburg. We are looking for two enthusiastic postdoctoral fellows in research and scientific software

Re: [ccp4bb] HKL2000 Display

2014-12-03 Thread David Waterman
Hi Muhammed, It looks a lot to me like denzo thinks your detector has a larger image size than the actual number of elements in the array. However, I don't use denzo so I'm not commenting from experience. Cheers -- David On 3 December 2014 at 04:09, Muhammed bashir Khan < muhammad.bashir.k...@u

Re: [ccp4bb] Intensities and amplitudes

2014-12-03 Thread Harry Powell
Hi Randy et al On 2 Dec 2014, at Tue2 Dec 22:46, Randy Read wrote: We could learn to embrace the R-factor on intensity that small molecule crystallographers are comfortable with but, as you say, people are not used to these. Small molecule crystallographers *still* prefer to talk about R-

[ccp4bb] Reminder - CCP4 Study Weekend 2015 - registration closes 14th December 2014

2014-12-03 Thread Karen McIntyre
The CCP4 Study Weekend (7 - 9 January 2015) East Midlands Conference Centre, University of Nottingham Wednesday 7 - MX User Meeting Thursday 8 / Friday 9 - CCP4 Study Weekend "Advances in Experimental Phasing" We cordially invite you to participate in the 2015 CCP4 Study Weekend at the the East