[ccp4bb] PhD Programme in Structural Biology in Vienna

*PhD Programme in Structural Biology in Vienna* The Medical University of Vienna (MUW), the University of Vienna (UNIVIE), the Research Institute of Molecular Pathology (IMP) and the Institute for Molecular Biotechnology (IMBA) announce the opening of an *International PhD Program in* ”*Struc

Re: [ccp4bb] mtz2various is broken [ was: Another pointless question ]

Thanks Ian - you have spotted the problem! I believe the Clipper routines must write out as a number the info flagged in the syminfo.lib as number 5 for example ( Spacegroup I 1 2 1) and not the info flagged as: symbol ccp4 4005 There are multiple space groups listed with the same number

Re: [ccp4bb] mtz2various is broken [ was: Another pointless question ]

> -Original Message- > From: Winn, MD (Martyn) [mailto:martyn.w...@stfc.ac.uk] > Sent: 12 June 2009 23:31 > To: Ian Tickle > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: RE: [ccp4bb] mtz2various is broken [ was: Another pointless > question ] > > > I didn't mean to commit to a particular solution

Re: [ccp4bb] How to sketch a cis double bond (carbon-carbon)

Hi Oliv, I'm sorry, I think you will need to edit the output file from Sketcher _mon_lib.cif - the torsions section ( _chem_comp_tor) will have something like test CONST_1 C1 C2 C3 C4 180.0 0.0 0 the 180 needs changing to 0.0. I think that is all you need to do - no doubt someone

Re: [ccp4bb] citrate blocks the active site

Dear Skkannu, since citrate is (a) necessary for crystal growth and stability and (b) blocks the active site I am afraid you will have to find a completely different crystal form. This means start screening all over again for crystallization conditions of your enzyme in the presence of a sufficient

[ccp4bb] Scientific software engineer post with EMDB at EBI

Dear colleagues: EMDB, the Electron Microscopy Data Bank at the European Bioinformatics Institute in Cambridge, England, has a staff position opening for a Scientific Software Engineer (Image Databases) We are looking for someone with very good software engineering skills (target platform is G

[ccp4bb] refmac 5.5.0092 not writing pdb/mtz files

Howdy, One of our users was trying to re-run some Refmac jobs originally run with version 5.5.0088 under version 5.5.0092, and he noticed that although the logfile shows Refmac completing successfully, the new version is not actually writing the pdb/mtz output files. He is using linux with CCP4

Re: [ccp4bb] How to sketch a cis double bond (carbon-carbon)

Hi Liz, Thanks a lot for pointing out the solution: indeed, this seems to be the only angle that needs changing in the _mon_lib.cif file. I tried that earlier and hoped that Coot magically could flip the bond by 180 degrees. This does not work and has to be done by hand, it seems. After that

[ccp4bb] quaternary structure comparison

Dear All, I solved a structure that has a very common tertiary structure motif but it appears as if the arrangement of the monomers is somewhat Œnon-standart¹. Of course I performed a DALI search, which resulted in a great number of hits due to the similarity of the tertiary structure (Z¹s: 250

Re: [ccp4bb] quaternary structure comparison

Hi Eike, PISA (http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html) or SCOPPI (http://www.scoppi.org ) might be useful. Interested in hearing about other alternatives. Best wishes Roberto On 15 Jun 2009, at 21:28, Eike - Christian Schulz wrote: Dear All, I solved a structure that has a very

Re: [ccp4bb] quaternary structure comparison

The human intelligance system "Alexey Murzin" of the LMB in Cambridge comes to mind - helpful and knowledgable about "all" known folds. Mark Quoting Roberto Steiner : Hi Eike, PISA (http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html) or SCOPPI (http://www.scoppi.org ) might be useful. Intere

[ccp4bb] combining phase information from a Se-Met and Hg SAD data sets

Hi, we collected SAD data sets to 3.0 A on our protein, once as a Se-Met protein and once soaked with a mercury compound. Data statistics indicate an anomalous signal in both data sets. However, the maps are not great. Is it possible to combine the phase information from the two data sets? We

[ccp4bb] open research assistant position at ImClone Systems

To anyone who might be interested: I have an opening in my group for a research assistant. The work will consist of cloning and protein expression, primarily using bacteria and insect cells, as well as protein purification and crystallization. I am ideally looking for someone with strong clon

Re: [ccp4bb] combining phase information from a Se-Met and Hg SAD data sets

On Mon, Jun 15, 2009 at 3:21 PM, Arnon Lavie wrote: > we collected SAD data sets to 3.0 A on our protein, once as a Se-Met > protein and once soaked with a mercury compound. Data statistics indicate an > anomalous signal in both data sets. However, the maps are not great. Is it > possible to comb

[ccp4bb] Multiple active or allosteric pocket allignment

Dear friends, Is it possible to allign structure of proteins of same class or family just based on acive site residues or defined by its volume of cavity with preferred deviation. any suggestions could possibly help me. sincerely S.Jayashankar Research Student Institute for Biophysical Chemis

Re: [ccp4bb] Multiple active or allosteric pocket allignment

Tue June. 16th 2009 EBI For example, FROFIT, where you can specify the residues involved in the actal alignment, and the residues to calculate the RMS on Miri On Tue, 16 Jun 2009, Jayashankar wrote: Dear friends, Is it possible to allign structure of proteins of same class or family just b