Re: [ccp4bb] determining the point group and the space group

Daniel, Gihan and all, please don't forget that the correct space group is ONLY determined once youhave ref ined the structure. Everything before is just an assumption. And there is many things that can fool you. Just to mention twinning, tNCS, etc. Therefore, when it comes to data collection fr

Re: [ccp4bb] determining the point group and the space group

Gihan, The best way, in my opinion, to choose a suitable (and correct) space group is to combine your own understanding and knowledge with the available software tools. I’ve never indexed XFEL data, so I don’t know if this data can be sampled and run through hkl2000/3000 or Mosflm to get some f

[ccp4bb] determining the point group and the space group

Hi, my question is; how should one determine a point group and the space group of an unknown crystal? I have a protein crystal with know unit-cell parameters. (these are XFEL data so indexing wouldn't give the point and space groups). I checked the PDB, but no luck the PDB structures have the d

[ccp4bb] Fully funded 4 year PhD position is available at University of Liverpool,UK/RIKEN, Japan

Dear all, Applications are invited for fully funded PhD studentship position in the laboratory of Prof Samar Hasnain (Liverpool,UK) in collaboration with Dr Masaki Yamamoto, Harima, RIKEN, Japan. The project involves the X-ray crystallography and X-ray Free-Electron laser study of proteins invol

[ccp4bb] Open PhD position in Oulu (Finland)

Dear all, we have an opening for a 4-year PhD student position in our lab in Oulu (Finland), and we are looking for good candidates (see link below). The project deals with structure-function analyses of mutations in several proteins linked to human peripheral neuropathies (Charcot-Marie-Tooth

Re: [ccp4bb] Cys Lys bond?

A similar bond is seen collagen; Met-Lys sulfilimine. Science 04 Sep 2009: Vol. 325, Issue 5945, pp. 1230-1234 Not sure if it helps, but in collagen the bond is conserved and not due to radiation damage. Ben Spiller On Apr 18, 2018, at 5:40 AM, Jonathan Davies mailto:jd...@bath.ac.uk

[ccp4bb] Robot for LCP (and regular low viscosity) setups

I hope this on not a duplicate/recent thread, apologies in advance… I am looking to acquire a crystallization robot and would like to know if anyone has strong preferences or pros/cons for any of these: Mosquito LCP Formulatrix NT8 Robbins Gryphon LCP Douglas Oryx Others? Thanks, Hudel -- Str

Re: [ccp4bb] Cys Lys bond?

Hi, Sulfilimine bond was identified in collagen IV using mass spec and NMR. https://www.ncbi.nlm.nih.gov/pubmed/19729652 Best, Abhishek On 4/18/18, Jonathan Davies wrote: > Dear All, > > > Thanks for all of the responses so far.. > > > Mark - I don't think it's caused by radiation damage, alth

Re: [ccp4bb] Cys Lys bond?

Dear All, Thanks for all of the responses so far.. Mark - I don't think it's caused by radiation damage, although this is certainly a concern. Using only a small subset of images from the start of data collection still gives fairly clear density with no positive or negative peaks around the

Re: [ccp4bb] merging an hkl file

Hi Gihan, Apart from Takanori's answer, you'll lose information in high resolution data as they usually tend to be this nature. This can introduce bias in the refinement. Rangana On Wed, Apr 18, 2018 at 12:27 AM, Gihan Ketawala wrote: > can someone tell me what are the posible consiquences of

Re: [ccp4bb] merging an hkl file

Hi Gihan, If you mean "sigma cutoff at 1" for reflection rejection criterion, don't do it! It is very biasing. See https://www.hkl.hkl-xray.com/alphabetical-scalepack-keyword-documentation#SIGMA%20CUTOFF for nice explanation why it is bad. This option is also present in process_hkl of CrystFEL. D

Re: [ccp4bb] merging an hkl file

Well - one usually integrates to the limit of the detector, and decides to cut the data on the basis of some snr then.. I/SigI > 1? Rpim < 100% ??? Up to you really.. Eleanor On 18 April 2018 at 10:37, Nicolas FOOS wrote: > I lkije the riddle, so: > > I guess it's something for Signal Noise

Re: [ccp4bb] merging an hkl file

I lkije the riddle, so: I guess it's something for Signal Noise Ratio (?)  (help by the context) ;-) Nicolas Nicolas Foos PhD Structural Biology Group European Synchrotron Radiation Facility (E.S.R.F) 71, avenue des Martyrs CS 40220 38043 GRENOBLE Cedex 9 +33 (0)6 76 88 14 87 +33 (0)4 76 88 4

Re: [ccp4bb] merging an hkl file

What does snr mean? Eleanor On 18 April 2018 at 00:27, Gihan Ketawala wrote: > can someone tell me what are the posible consiquences of merging only the > reflection are snr >= 1 ? >

[ccp4bb] Computational Postdoctural Opening at Birkbeck College, London

Hi all, * * * * *We have a Postdoctoral Researcher (Bioinformatics/Data Bases/Computer Science/Structural Biology) position in the Wallace lab which is part of the Birkbeck/UCL Institute of Structural and Molecular Biology in London.* Full Time, fixed-term post, initially for one year, with