[ccp4bb] Nomenclature Re: [ccp4bb] Structures determined: breakdown of methods

Dear James, Thankyou for this interesting summary analysis. Just at the end of your message I would remark about "nomenclature". I meant to reply before in a recent thread about resolution terminology issues but was focussed on CCP4. So, just to say that as a community we have three categories o

[ccp4bb] Synchrotron Beamline Facilities 2011 at EMBL Hamburg

Call for access to Synchrotron Beamline Facilities 2011 EMBL Hamburg, Germany We announce a call for synchrotron beam time applications in biological small-angle scattering (SAXS) and X-ray crystallography (PX). Up to 32 weeks of beam time will be available at the DORIS stora

Re: [ccp4bb] Structures determined: breakdown of methods

On 1/15/2011 12:28 PM, REX PALMER wrote: Does anyone know of a statistical breakdown of successful protein structure determinations in terms of the method used? Rex Palmer Birkbeck College I think this was discussed back in April under "Proportion of MR in PDB": https://www.jiscmail.ac.uk/cg

Re: [ccp4bb] Refmac: sidechain bond breaks

Marcus, it appears that coot "breaks" bonds when the distance between atoms exceeds 1.64A pretty much irrespective of the bond type. Two exceptions are, of course, sulfurs in MET/CYS. CB-SG bond in cysteine does not seem to have any cutoff (when you do rotate/translate zone in coot, you can move

Re: [ccp4bb] how to generate density map of selected residues

Hello Michael and others, Sorry that my statement did cause some confusion. There is nothing wrong with the carve option as such. I also use it very regularly. It is only the way of using which matters. If you have good density and carve at a sufficient distance around your region of interest,

Re: [ccp4bb] phaser MR hiccup

Hi Eleanor, A bit more context about what Phaser was doing at the time might help... As a first guess, it looks like there was an odd character in a text file (PDB file?). Do you have a PDB file with funny line terminators or something like that? Regards, Randy On 17 Jan 2011, at 11:50, Ele

[ccp4bb] phaser MR hiccup

Does anyone know where to look for an error when PHASER outputs this message? Eleanor . * *** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.1.4 *** ***

[ccp4bb] extension of deadline for abstract submission

To all UK Young Crystallographers, The deadline for submitting oral abstracts for the YC Satellite Meeting at the BCA Spring Meeting has just been extended to Friday 21st January! So if you haven't done so submit your abstracts NOW! Deadline for poster abstracts is still 4th February. The YC S

Re: [ccp4bb] Refmac: sidechain bond breaks

Dear Marcus The most likely reason is that geometry is a bit loose. You need to tighten it a bit. You can do by decreasing weight using weight matrix option on the interface. You need also check the electron density to make sure that ILE is in electron density. Please let me know if you hav

Re: [ccp4bb] rebatch abort

Not without running it under the debugger. Since this is my program I suppose I should look at it (if you send me the file) Phil On 17 Jan 2011, at 11:17, James Foadi wrote: > Dear CCP4ers, > does anyone understand where the problem is? The run is from the program > rebatch. > Keywords are: >

[ccp4bb] rebatch abort

Dear CCP4ers, does anyone understand where the problem is? The run is from the program rebatch. Keywords are: TITLE Rebatch file for multicrystal merging BATCH 3 TO 15 REJECT BATCH ALL START 1 END Log file follows: REBATCH #

[ccp4bb] PhD offer

A 3year PhD thesis fellowship financed by the French Atomic Energy Commission and entitled "Study of photoactivatable fluorescent proteins for super resolution imaging" is to be had for autumn 2011. Description: Super-resolution fluorescence imaging has recently revolutionized cell biology, bec

Re: [ccp4bb] Refmac: sidechain bond breaks

Well - REFMAC and I think other refinement programs simply read in an atom with occupancy 0.00 and write it out again in exactly the same place.. All refinement contributions for atoms both Xray and geometrical are weighted by the atom occupancy so such an atom will not shift. The assumption i

[ccp4bb] Refmac: sidechain bond breaks

Dear all, I might excuse myself for the silly question but it is the first time I solve an x-ray structure. After modell building in coot and running of refmac with restrained refinement I have the problem that the pdb output file contains distances between e.g. ILE Cb and Cg that are so long tha

[ccp4bb] Postdoc Position in Dundee, UK

Dear All, The following postdoc position is posted on behalf of Bill Hunter. All enquiries should be made to w.n.hun...@dundee.ac.uk. Reference Number: LS0037 Job Title: Postdoctoral Research Assistant College: