[ccp4bb] Postdoctoral position - London UK - apply by 20 May 2021

th). 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 fr

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 introduci

Re: [ccp4bb] Why there are difference density when occupancy is 1.00

pinions and suggestions! > > Best wishes, > > Sun Tang > > > - > Never miss a thing. Make Yahoo your homepage. -- Sent from Gmail for mobile | mobile.google.com Dr. James Irving NH&MRC C.J. Martin Fellow School of Biomedical Science

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, includin

Re: [ccp4bb] CNS v1.2 and unwanted introduction of OXT

Hi Fred, From memory, this can occur due to long bond lengths in the model being interpreted as chain breaks, try editing the generate.inp or generate_easy.inp script and increase the value for "break_cutoff": {* cutoff distance in Angstroms for identification of breaks *} {* the default of 2

Re: [ccp4bb] how many stuck datasets are actually twinned?

I guess the point is to "know thy data", to avoid problems down the track: a statistical test for twinning forms one of a battery of tests which can be performed independently of a coordinate set (Matthews coefficient, self-RF, etc.), and with relative ease. Importantly, in the case of partial

Re: [ccp4bb] to detwin the twinned data

th 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 NH&MRC C.J. Martin Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Oxford University R

Re: [ccp4bb] Colour surface by sequence conservation

db' file). I get the error: 'Fatal error: wrong format in PDB file.' ..and the values in the B-factor (%Equivalent) column are all either 99 or 100 which is nonsense according to the alignment. Has anyone come across this. I don't see anything wrong with my PDB file.. Thanks,

Re: How to find a third or maybe fourth molecule in MR?

Hi Jenny, As you have a trigonal/hexagonal spacegroup, have you eliminated the possibility of twinning? This can create ghosts in the density... Cheers, James