Re: [ccp4bb] Fwd: Crystallographic Software Fayre (ECM27, Bergen)
Dear all The deadlines below have been extended to 15th June. Note that, since the deadline for abstracts is still open, there should still be the opportunity of having your work chosen to be an oral presentation (three of the five talks in MS are chosen from the abstracts). The lists of speakers have not yet been finalised (how can they be when the abstract submission process is still open?), but a taster of some of the talk titles and speakers in a few of the MS is listed at - http://sig9.ecanews.org/sig9_activities.html Students of history may be interested to learn that Bergen was apparently founded by the son of Harald Hardrada, the Norwegian king who was killed at the battle of Stamford Bridge in 1066, just over a fortnight before a seminal moment in English history. On 22 May 2012, at 15:08, Harry Powell wrote: Hi folks The list of microsymposia at ECM27 is now available, but the list of speakers has not yet been finalised. Bear in mind that earlybird registration closes on 31st May, when the cost jumps by 750 NOK (~€100) for full participants, 550NOK (~€72) for students. The meeting website is http://ecm27.ecanews.org/ On 11 May 2012, at 10:36, Harry Powell wrote: Hi folks Any of you who are considering attending ECM27 in Bergen may be interested in some of the sessions that have been arranged at this Software Fayre. The full list of Microsymposia at ECM27 should be available in the next couple of days From: Martin Lutz m.l...@uu.nl Date: 10 May 2012 13:48:11 GMT+01:00 To: undisclosed-recipients:; Subject: Crystallographic Software Fayre (ECM27, Bergen) Dear all, thanks to the local organizers, there will be a Crystallographic Software Fayre at the ECM27 meeting in Bergen (Norway). Authors of of academic and/or open-source software can present their new developments. The presentations should have a tutorial character with one or more practical examples. The available time slots can be seen on the website: http://www.cryst.chem.uu.nl/lutz/software_fayre.html (This website will be updated regularly) If you are interested, please send an e-mail with your name and a preliminary title of the presentation to Martin Lutz, m.l...@uu.nl. The time slots will be filled according to the first-come first-served principle. For information about the ECM27 congress (August 6-11, 2012), see: http://ecm27.ecanews.org With kind regards, Martin (Please forward this e-mail to anyone, who might be interested.) -- Martin Lutz Crystal and Structural Chemistry Bijvoet Center for Biomolecular Research Faculty of Science Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands Tel. [+31] 030-2533902 Fax [+31] 030-2533940 Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
[ccp4bb] CME
Dear All, I have one query while fitting residues into the density i came across the cysteine residue which as per me is fitting nicely as Cys in disulfide bond with beta mercaptoethanol, so from coot i have taken CME which is infact cysteine plus bme, my query is how to proceed with submission, can i show it as a modified residue CME or cys in disulfide bond with bme. -- Regards Faisal School of Life Sciences JNU
[ccp4bb]
In my experience, occupancies and B-factors are correlated for small molecules, e.g. waters and here I keep the occupancy at 1.00 and only refine B-factors. However, for larger ligands e.g. Cl-, Zn2+ etc. often a shell of red difference density around the ion indicates to me that occupancies and B-factors do not fully compensate each other. Also, as a ligand is either present or gone, it only makes sense to refine group occupancies, which, again in my experience (Buster) produces quite sensible results, even at 2.2 Å. In fact, I now refine group occupancies for everything which is not water and not covalently in full occupancy attached to the protein, e.g. metal ions, chloride, phosphate, sulfate etc. even at resolutions lower than 2.2 Å. Cheers, Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Katherine Sippel Sent: Monday, June 04, 2012 8:11 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Hi Ed, I've actually run that exact test in phenix as an exercise to prove to my PI the validity of occupancy refinement. Though as a disclaimer it was a 1.2 angstrom data set and this was an alternate conformation situation. I ran different input occupancies without occupancy refinement and measure the difference density peak values and average B-factors and ended up with the same occupancy ratio that the program's occupancy refinement spit out. Of course this might not hold true if someone is refining the occupancy of a ligand that is partially bound without an alternate option (i.e. total occupancy 1). I haven't tested that one systematically yet though I suspect Pavel has probably already done this at some point. Cheers, Katherine On Mon, Jun 4, 2012 at 7:35 AM, Ed Pozharski epozh...@umaryland.edu wrote: Is it reasonable to refine occupancy in phenix at 2.2 A resolution? Implementations may differ, but imgo refining occupancy at 2.2A resolution is not very reasonable under most circumstances, as it will correlate strongly with the B-factor. A reasonable approach might be to fix occupancy at different levels and get a series of refined models. Then you look at (i) B-factor behavior and see at what occupancy it matches the surrounding atoms and (ii) difference density (my unsubstantiated theory is that if you plot it against occupancy it should have a central flat region where B-factors are capable of compensating and two linear regions on extreme ends which should allow to extrapolate the true value. Refmac does occupancy refinement. It's quite fast, so you may try randomizing the initial value and get some idea about convergence. Cheers, Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] CME
On Tue, 2012-06-05 at 15:26 +0530, Faisal Tarique wrote: how to proceed with submission, can i show it as a modified residue CME or cys in disulfide bond with bme You can do either. One could potentially argue that cys+bme is more appropriate since the protein presumably had cysteine which was modified, not cme residue incorporated during protein synthesis.
[ccp4bb] difference between PEG 4000 and polyacrylate 5100
Dear ALL; Both PEG and polyacrylate are polymers. Although their formulations are different, Could they be exchangeable in crystallization conditions? Thanks a lot, Jerry McCully
[ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Hey! I was just wondering, do you know of any recent (~10y) publication that presented a structure solution solely based on MIR? Without the use of any anomalous signal of some sort? When was the last time you saw a structure that was solved without the use of anomalous signal or homology model? Is there a way to look up the answer (e.g. filter settings in the RCSB) I am not aware of? Thanks, S. (Disclaimer: I am aware that isomorpous data is a valuable source of information)
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
On Tuesday, 05 June 2012, Stefan Gajewski wrote: Hey! I was just wondering, do you know of any recent (~10y) publication that presented a structure solution solely based on MIR? Without the use of any anomalous signal of some sort? A text search for MIR returns 1377 PDB structures overall. Of these 706 were deposited in the last 10 years, and 34 were deposited in the last 12 months. The most recent was released today (6 Jun 2012) HEADERHYDROLASE 17-APR-12 4EPC TITLE CRYSTAL STRUCTURE OF AUTOLYSIN REPEAT DOMAINS FROM STAPHYLOCOCCUS REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL Caveats: I have no idea how many of those structures say MIR because it's part of the protein name or some such, I have no idea how accurate the REMARK 200 fields are in any case, and I don't really trust the www.pdb.org search interface in general. When was the last time you saw a structure that was solved without the use of anomalous signal or homology model? Is there a way to look up the answer (e.g. filter settings in the RCSB) I am not aware of? Thanks, S. (Disclaimer: I am aware that isomorpous data is a valuable source of information)
