[ccp4bb] Postdoctoral position - London UK - apply by 20 May 2021
Dear all, We have a postdoctoral opportunity available in our laboratory in a collaboration with the groups of Prof. John Christodoulou (UCL) and Prof. Angela Russell (Oxford). The successful applicant will be working within a vibrant research precinct in central London at the Bloomsbury campus of UCL. They will apply their structural biology expertise to drive a project that aims to develop a conformation-selective small molecule reporter of pathogenic forms of alpha-1-antitrypsin. Recent relevant publications include Jagger et al Nat Commun 2020 (doi: 10.1038/s41467-020-20147-7), Faull et al Science Adv 2020 (doi: 10.1126/sciadv.abc1370) and Lomas et al EMBO Mol Med 2021 (doi: 10.15252/emmm.202013167). The full job description can be found at: https://atsv7.wcn.co.uk/search_engine/jobs.cgi?owner=5041553=fair=1876144 (application deadline May 20th). I'm happy to answer informal enquiries at j.irv...@ucl.ac.uk. Best wishes, James Dr. James Irving UCL Respiratory / Institute of Structural and Molecular Biology University College London London UK To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Perfect twins.
Hi Francis, Detwinning of perfectly twinned data is done with reference to Fcalc (determined from from the model): it is not possible to arithmetically deconvolute the contribution of the twin domains to the perfectly twinned reflection data. Because your model is incomplete you will be introducing (or subject to) significant bias by refining against the resulting incompletely/inaccurately detwinned data. The solution is to use minimize_twin.inp/anneal_twin.inp (CNS) or phenix.refine twinning.twin_law=xxx (PHENIX) to perform the refinement in the true space group on the original data, taking into account the twin operator. The map produced by model_map_twin.inp (and presumably phenix.refine) will still be based on data detwinned with reference to the model, but at least this occurs post-refinement. One way to limit a molecular replacement search to one twin domain is to perform the rotation search in the apparent space group and the translation search in the true space group. If the result is more than one molecule in the asymmetric unit, NCS is certainly useful because perfectly twinned data halves the number of independent reflections (and hence the data-to-parameter ratio). Test set (rfree) reflections should also be chosen taking into account the twin operator, for example with make_cv_twin.inp in CNS. HTH, James
Re: [ccp4bb] PERL system call to CCP4
You can check whether something strange is happening to your environment variables within the PERL process by typing:perl -e 'print join(\n,%ENV).\n' | more hth
Re: [ccp4bb] How to make a structure-based multiple sequence alignment on DALI server?
You can perform a multiple structural alignment using MUSTANG ( http://www.bx.psu.edu/arun/research/mustang/), which draws upon some of the underpinnings of the DALI approach. James
Re: [ccp4bb] twwining operator
Hi Siva, SFCHECK (part of CCP4i) has a very handy option for this. From the command line: % mkdir mydir % sfcheck -f mydata.mtz -po mydir/ -out u -r % gv mydir/sfcheck_.ps (or ghostscript/xpsview/whatever postscript viewer you have) This will generate a number of output files, including a useful postscript summary of your data (including twinning operator and fraction, if detected). If twinning is detected sfcheck will also output a detwinned dataset (sfcheck.hkl) which is in CIF format - although at least with my version before you convert the CIF to MTZ in CCP4i, you have to change the line in the .hkl file that reads _refln.F_meas_au_sigma to _refln.F_meas_sigma_au. However, unless your twinning fraction is low and your data behaves well under detwinning, I would suggest using the twinned data as is, in SHELX, CNS or PHENIX. Best of luck, James siva charan wrote: hello I have a data set to 2.4 A, which has space group of *P21 *. From the cumulative intensity distribution graph, indicates that data is twinned . To run the detwin program in ccp4, one has to know the twinning operator. Can anybody help me, how can I get the twinning operator for monoclinic space group. I have checked for twin operators at http://www.ccp4.ac.uk/dist/html/twinning.html, but there are no twining operators for monoclinic space group. regards siva
Re: [ccp4bb] to detwin the twinned data
shivesh kumar wrote: Dear all, Can u suggest me any method to detwin the twinning data(2.2A).Any suggestions are welcome.Thanx in advance. Shivesh Hi Shivesh, For a partially twinned dataset with a twinning fraction not too close to 0.5, from the command line: % mkdir my_dir % sfcheck my_dir/ FILE_F my_twinned.mtz OUT U TEST Y blank line This will create a detwinned dataset in the my_dir directory in mmCIF format (with an .hkl extension). Check the sfcheck_.ps postscript file for details. Import into ccp4i using the 'convert to MTZ' option under 'Reflection utilities' from mmCIF format. If there is an import error, manually edit the .hkl file, changing _refln.F_meas_au_sigma to _refln.F_meas_sigma_au. SHELX can refine the structure and the twinning fraction simultaneously; you may want to consider this. A dataset with a partial twin fraction close to 0.5 or perfectly twinned should not be detwinned, use SHELX or CNS to refine against the twinned data instead. HTH, James -- Dr. James Irving NHMRC C.J. Martin Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Oxford University Roosevelt Drive, Oxford OX3 7BN UK email: [EMAIL PROTECTED] phone: +44 1865 287 550
