Re: [ccp4bb] ionic interaction inside a protein
The link is fine. If you still get the 'error message', then google PIC webserver , fullform of PIC - protein interactions calculator. Seema Nath
[ccp4bb] cell disruptor / homogenizer
Dear colleagues, We are currently looking for new cell disruptor/homogenizer equipment, mainly for E.coli work. We currently have a Branson sonifier and a Microfluidics Fluidizer - the latter one keeps causing trouble, and we think about a replacement. We previously also used an Avestin C-5 Emulsiflex, required quite some maintenance, and I inquired about a Constant Systems TS 0.75 and got mixed responses from users (not to mention their outrageous pricing). My question: What is your experience with Fluidizer, Emulsiflex, TS 0.75? Is there any other great (low maintenance, affordable - especially concerning follow-up costs: repairs, replacement parts) equipment I missed? Thanks in advance for your comments Best regards Clemens
Re: [ccp4bb] cell disruptor / homogenizer
Dear Clemens, I used the Panda homegenizer (GEA Niro Soavi) to disrupt E.coli cells: is really good, I always did the maintenance on my own, is not very expensive and easy to use. I found bigger models also in the big pharmas...so is really reliable. http://www.niro-soavi.com/home.html Hope to be helpful. Cheers, Barbara On Mon, 25 Mar 2013 10:16:55 +0100 Clemens Steegborn clemens.steegb...@ruhr-uni-bochum.de wrote: Dear colleagues, We are currently looking for new cell disruptor/homogenizer equipment, mainly for E.coli work. We currently have a Branson sonifier and a Microfluidics Fluidizer - the latter one keeps causing trouble, and we think about a replacement. We previously also used an Avestin C-5 Emulsiflex, required quite some maintenance, and I inquired about a Constant Systems TS 0.75 and got mixed responses from users (not to mention their outrageous pricing). My question: What is your experience with Fluidizer, Emulsiflex, TS 0.75? Is there any other great (low maintenance, affordable - especially concerning follow-up costs: repairs, replacement parts) equipment I missed? Thanks in advance for your comments Best regards Clemens Barbara Giabbai Elettra-Sincrotrone Trieste S.C.p.A. SS 14 - km 163,5 AREA Science Park 34149 Basovizza, Trieste ITALY Office: +39 040 375 8840 Lab: +39 040 375 8537
[ccp4bb] Software developer position
Dear All A Software Developer position is currently available in my laboratory at EMBL Grenoble. You will find the details in the link below or at www.embl.org/jobs http://www.embl.fr/aboutus/jobs/searchjobs/index.php?newlang=1newms=srsearchregion=670 http://www.embl.fr/aboutus/jobs/searchjobs/index.php?newlang=1newms=srsearchregion=670 http://www.embl.fr/aboutus/jobs/searchjobs/index.php?newlang=1newms=srsearchregion=670 Location: Grenoble, France Staff Category: Staff Member Contract Duration: 1 year Grading:4, 5 or 6, depending on experience and qualifications Closing Date: 07 April 2013 Reference number: GR_00052 Best regards Josan -- _ Jose A. Marquez Ph.D. Team Leader, Head of Crystallization Facility EMBL Grenoble Outstation Postal address: EMBL Grenoble Outstation, 6 Rue Jules Horowitz, BP181 38042 Grenoble Cedex 9, France Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 6 Rue Jules Horowitz 38000 Grenoble, France Phone +33 (0)476 20 74 25 Fax. +33 (0)476 20 71 99 https://embl.fr/htxlab/ __ attachment: marquez.vcf
[ccp4bb] Call for targets of biomolecular complexes for CAPRI
Members of this mailing list may be in a position to help with targets for the next Critical Assessment of PRediction of Interactions . CAPRI (Critical Assessment of Predicted Interactions) is a community-wide blind experiment aimed at assessing the performance of protein docking algorithms (http://www.ebi.ac.uk/msd-srv/capri/) [1,2]. CAPRI acts as a catalyst for the development of computational methods for the prediction and analysis of biomolecular interactions. We call here upon the worldwide structural biology community to contribute targets to CAPRI. If you have solved or are about to solve the 3D structure of a protein-protein, protein-DNA, protein-RNA or protein-peptide complex, you may consider submitting your structure as a target to CAPRI. By doing so, you will contribute to advancing the methodology. This may also provide you with new information on the quaternary structure of your complex and will increase the visibility of your work since CAPRI participants are requested to duly cite the provenance of all targets. CAPRI is designed to maintain strict confidentiality on the target and imposes no delay on its publication, as the experiment is running whenever a new target is submitted, prior to any public release of the coordinates to the PDB and publication. To enable this, the coordinates should be made available to the CAPRI assessment team on a confidential basis prior to their release. To find out more about CAPRI target submission see: (http://www.ebi.ac.uk/msd-srv/capri/call_for_targets.html ), or directly contact the CAPRI management team via Prof. Dr. Shoshana Wodak at shosh...@sickkids.ca We thank you for your contribution to CAPRI. The CAPRI committee • Alexandre Bonvin(Utrecht University, the Netherlands) • Joel Janin (Prof. Emeritus, Université Paris-Sud, Orsay, France) • Marc Lensink(CNRS, University of Lille I, France) • Michael Sternberg (Imperial College London, UK) • Sandor Vajda(Boston University, Boston, USA) • Ilya Vakser (The University of Kansas, Lawrence KS, USA) • Sameer Velankar (EBI, Hinxton, UK) • Shoshana Wodak (University of Toronto and Hospital for Sick Children, Canada) • Zhiping Weng(University of Massachusetts Medical School, Worcester MA, USA) References 1. Lensink M.F., Wodak S.J. (2010).Docking and scoring protein interactions: CAPRI 2009. Proteins 78(15):3073-3084. 2. Janin J, Wodak S. (2007). The third CAPRI assessment meeting Toronto, Canada, April 20-21, 2007. Structure 15(7):755-759.
[ccp4bb] השב: Re: [ccp4bb] Vote for crystallography
Well done to you Fred for pointing this out to us. How did you comr across it? Cheers, Boaz נשלח מהטלפון הנייד של Samsung הודעה מקורית מאת: vellieux frederic.velli...@ibs.fr תאריך: אל: CCP4BB@JISCMAIL.AC.UK נושא: Re: [ccp4bb] Vote for crystallography Dear all, I couldn't help having a look at the results of the top innovations census (results to be announced today). Enclosed herewith is a small jpeg file (sorry about the attachment but I made sure the file is small) with a screen capture (from this morning) showing what I think will be the results of the vote: X-ray crystallography ranks number 3. So it appears that our science is viewed as important by the public - rightly so. Crystallography gathered 10 % of the votes. Hurray ! A nice (crystallographic) day to all, Fred. -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: 33 438789605 Fax: 33 438785494
Re: [ccp4bb] molecular replacement problem.
Umm - this is tricky. First of all you need to reindex the C2221 data into the P21 cell - do you know the operator? then expand that data set to spacegroup P21. There is a cad option to do this.. Then add that FreeR to the re-processed P21 data. Eleanor On 24 March 2013 14:37, Appu kumar appu.kum...@gmail.com wrote: Sorry for the misconception. Yes i am expanding the space group from merged mtz file. Actually i have enough number of images collected. when i indexed, integrate, and scale the data in either C2221 or P 21, it fetches the overall 98% completeness. But when i am trying to reindex the data from C2221 to P21 keeping the Rfree flag of C2221, the completeness of data reduced drastically to 40%. This is what i am not getting. I am a beginner so i have to read a lot which i am doing also, but i had few practical confusion which i shared and off course i am getting good response. Thank you all for your kind response and educating me on the problem i faced. Thank you all for your valuable response. On 24 March 2013 15:15, vellieux frederic.velli...@ibs.fr wrote: Hello, Here we deal with symmetry and the unique part of reciprocal space (the reciprocal space asymmetric unit so to speak). C222(1) has eight asymmetric units (international tables, space group 20); P2(1) only has two. Assuming that Friedel's law does apply, then the minimum rotation range to collect a non-redundant data set (one observation per reflection) is 90 degrees, provided that the crystal is correctly and perfectly aligned. Normally with our current data collection methods where the crystal is randomly oriented, we would collect more than 90 degrees (180 degrees, or 360 degrees with the Pilatus detectors on an intense SR beamline where you cannot really check during data collection how well the crystal fares during exposure to the X-rays - shoot first, think later. The reciprocal space asymmetric unit in C222(1) is smaller. I assume that what you are doing is to take the reduced data set file (an MTZ file probably) and reduce the symmetry from C222(1) to P2(1). You will not cover the monoclinic reciprocal space asymmetric unit by doing so. The way to do it is to take the file from processing, before (crystallographic symmetry) merging of the equivalents, and perform the scaling and merging in the P2(1) space group. Or reprocess the data frames in P2(1) if you have lost the unmerged data file. Now of course this will still give you a poor completeness if you have used a strategy to optimize data collection in the orthorhombic space group (you won't have collected enough data then for good completeness in the monoclinic space group). I hope this is clear ! HTH, Fred. On 24/03/13 11:20, Appu kumar wrote: I run the phenix.xtriage to evaluate the twining but it suggest no twining. When i reindex from C2221 to P21, the completeness of data reduced from 95 % to 35% whereas the map is very good and Rwork and Rfree are 26/31 for 2.2 resolution. I do not understand why the completeness of data reduced so much on reindexing. please Can anyone explain this phenomenon. Thank you On 24 March 2013 13:30, Matthias Zebisch matthias.zebi...@bbz.uni-leipzig.de wrote: the p21 c2221 ambivalence can mean severe twinning (i had a similar case just now - try several crystals from the same condition) ! What do the twinning statistics suggest? cheers, Matthias - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk Website http://www.strubi.ox.ac.uk - On 3/24/2013 7:46 AM, Appu kumar wrote: Thank you for the quick reply. After molecular replacement , i have done only few cycle of refinement in refmac. I have not done any solvent modification or NCS averaging. I have initially indexed the data in C2221 but Rfree was not decreasing so i reindexed the data in data in P121 space group keeping the Rfree flag of C2221. While analysing the symmetry mates , i found large space but no density. structure of Ligand binding domain is almost identical with 90% identity in sequence. I am stuck with this problem and don't know how to process further. Please give me your valuable suggestion. I will appreciate your effort. Thank you Appu On 24 March 2013 02:38, Raji Edayathumangalam r...@brandeis.edu wrote: Dear Appu, I am not sure that I have a complete sense of the issue at hand since some of the information needed to think your issue through is missing in your email. For example, to what high resolution cut-off were the data measured? What resolution limits were used for the MR search? How do the unit cell dimensions and space group in the two cases compare? I am guessing the ligand binding
Re: [ccp4bb] ionic interaction inside a protein
Thanx everybody..PICserver is really good On Mon, Mar 25, 2013 at 12:09 PM, Seema Nath seema.n...@saha.ac.in wrote: The link is fine. If you still get the 'error message', then google PIC webserver , fullform of PIC - protein interactions calculator. Seema Nath -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] Strange density in solvent channel and high Rfree
First - I dont think you have a 3rd molecule where you have put it - or at least not one with full occupancy. Those maps are a clear indication that something is wrong. What is the Matthews coefficient for the numbers in the asymmetric unit? Presumably your processing gave you a lattice which fitted the diffraction spots? ie you didnt miss a set of observations? You should see that at the data processing stage, and the different integration programs also try to report it. If there is non-crystallographic translation that can confuse things a bit; some classes of reflections might be systematically weak, but you can find if there is such a phenomena by doing a patterson. Or run ctruncate after merging the data - it checks this, and so does Xtriage. All these options will also check for twinning. If there is NCT then that could explain the high Rfactor. Are the spots nicely shaped? There are some cases of sheared crystals, which usually show up in distorted diffraction spots. If this is so and you have integrated the data according to an orthogonal lattice, there is nothing to stop you merging those observations in a low symmetry. Pointless gives you good statistics on the scoring for different symmetry operators. You can either run MR again in that symmetry - check all SGS consistent with the pointgroup, or try to work out how to position your P22121 solution in the new SG. There may well be 2n+1 copies of your molecule when you double the size of the asymmetric unit - all hard to check without more information. Good luck Eleanor On 22 March 2013 17:54, Andrey Nascimento andreynascime...@gmail.comwrote: Dear all, I have tried the procedure recommended by Zbyszek, expanding data from a higher symmetry and keeping the R-free set. But the map for third molecule (new molecule placed) are still very bad, even when a tried to reprocess data in P1 or P2 (P 1 21 1). The previous placed molecule (present in P2 21 21 ASU) and its symmetry related on P21 shows a very good map, but the third molecule are almost completely wrong (~50 residues in 470 are placed in quite good map) and map does not have connectivity to build a new molecule (even in lower sigmas, 0.8-1.0). I have tried automatic model building (AutoBuild and ARP/wARP) but they cannot build anything that make some sense or build a random chains without any sense. I do not have an extensive knowledge of crystallography, but I have been thinking about some questions: If the third molecule (the bad one) is lying on the 2-fold symmetry axis on P 2 21 21, and since it does not have an intrinsic 2-fold symmetry axis (like protein molecule), how can I merge the structure factors (or intensities) related by symmetry and expand to lower symmetry afterwards? In this case the molecule lying on the 2-fold symmetry axis will have the structure factors wrongly merged, since the molecule is not symmetric, is it ok? If the third molecule is lying on the 2-fold symmetry axis on P 2 21 21, and only another two molecules can be related by the crystallographic symmetry, is it a case of pseudo-symmetry? But in this case, the third molecule is disordered in the crystal packing (as Zbyszek said), and probably have a long range disorder, because I cannot get a good maps for this third molecule even in P1. (pseudo-symmetry + order/disorder). And a more philosophical question… what is the problem in process data in a lower symmetry? Are there mathematical/statistical problems related that can lead to “false-good” data? I put a new .pdf file (ccp4bb_maps_P21.pdf) with map figures in this link: https://dl.dropbox.com/u/16221126/ccp4bb_maps_P21.pdf I am sorry for so many questions and thanks in advance. Cheers, Andrey 2013/3/20 Jrh jrhelliw...@gmail.com Dear Zbyszek, I am concerned that the unmerged data would be bypassed and not preserved in your recommendation. I also find it counter intuitive that the merged data would then be unmerged into a lower symmetry and be better than the unmerged data; there is I imagine some useful reference or two you can direct me to that may well correct my lack of understanding. Thirdly I think this a very likely useful case to preserve the raw diffraction images. All best wishes, John Prof John R Helliwell DSc On 19 Mar 2013, at 14:37, Zbyszek Otwinowski zbys...@work.swmed.edu wrote: It is a clear-cut case of crystal packing disorder. The tell-tale sign is that data can be merged in the higher-symmetry lattice, while the number of molecules in the asymmetric unit (3 in P21) is not divisible by the higher symmetry factor (2, by going from P21 to P21212). From my experience, this is more likely a case of order-disorder than merohedral twinning. The difference between these two is that structure factors are added for the alternative conformations in the case of order-disorder, while intensities (structure factors squared) are added in the case of
