[ccp4bb] coot - how to define a keyboard shortcut for "update NCS ghosts with local match" ?
Hello, I like the function "update NCS ghosts with local match" found in the calculate/NCT tools menu. It's really helpful when NCS is not really strict. However, I find it clumsy that you have to go in a submenu to get it, so I would like to define a keyboard shortcut... this would be much faster. Which function should I use to do that ? (add_key_binding "Update ghosts" "a" (unknown function) thanks a lot ! Laurent -- logo-ipbs Laurent Maveyraud Professor of Biophysics | University of Toulouse Doctoral School Biology - Health - Biotechnologies +33 5 61 17 54 35 | +33 6 46 04 21 11 | laurent.maveyr...@ipbs.fr <mailto:laurent.maveyr...@ipbs.fr> UMR5089 | CNRS - UT3 | 205 Route de Narbonne BP 64182 - 31077 Toulouse Cedex 4 ipbs.fr <https://www.ipbs.fr> @IpbsToulouse <https://twitter.com/IpbsToulouse> ipbs.cnrs <https://www.facebook.com/IPBS.CNRS/> our group <https://www.ipbs.fr/structural-biophysics> <https://orcid.org/-0003-4610-8319> <https://www.linkedin.com/in/laurent-maveyraud-8b394a5/> <https://www.linkedin.com/in/laurent-maveyraud-8b394a5/> <https://www.linkedin.com/in/laurent-maveyraud-8b394a5/> <https://www.linkedin.com/in/laurent-maveyraud-8b394a5/> <https://www.linkedin.com/in/laurent-maveyraud-8b394a5/> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] CCP4BB Digest - 21 Dec 2023 to 22 Dec 2023 (#2023-324) (out of office)
Thank you for your e-mail. I am out of office until January 2nd, 2024. I will respond to your e-mail as soon as possible upon my return. For urgent matters please contact: b...@boku.ac.at Thank you for your understanding. With kind regards, Elisabeth Laurent >>> CCP4BB automatic digest system 23.12.23 01:00 >>> There are 4 messages totaling 667 lines in this issue. Topics of the day: 1. Two-year postdoctoral position in time-resolved crystallography at IBS in Grenoble 2. Postdoc opportunity at the PSI of Switzerland. 3. Relion issue with MPI 4. Relion issue with MPI To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- Date:Fri, 22 Dec 2023 10:20:57 +0100 From:Elke De Zitter Subject: Two-year postdoctoral position in time-resolved crystallography at IBS in Grenoble Dear all, We have an immediate opening for a two-year postdoctoral researcher in SNaX team of the DYNAMOP group at the Institute for Structural Biology in Grenoble (France). The successful candidate will work on the development and optimization of bio-scavengers towards toxic organophosphorus compounds. To attain this goal, the researcher will use time-resolved crystallography and in silico protein design methods. The position is funded by the French National Research Agency via the University Grenoble Alpes, and is open for a young researcher. Applicants must have obtained a Ph.D. in structural biology, biochemistry, biophysics, physics, chemistry, or a related field, no more than two years before the start of the project. The candidate must show a track-record of publications in peer-reviewed journals, and is expected to be proficient in English and highly motivated to learn new skills. The candidate will work in the multidisciplinary DYNAMOP group and thus needs to be a good team player as well as being capable of working independently. While the research will be carried out in English, non-French-speaking candidates are expected to learn the basics of French in order to facilitate communication and integration into the laboratory. Experience with one or more of the following skills would be highly evaluated: protein design or the usage of artificial intelligence for structural biology, protein expression and purification, protein crystallization and macromolecular crystallography, serial crystallography, programming or scripting. Interested candidates can apply via [ https://emploi.univ-grenoble-alpes.fr/offres/doctorants/postdoctoral-researcher-in-time-resolved-crystallography-1357683.kjsp?RH=1135797159702996 | https://emploi.univ-grenoble-alpes.fr/offres/doctorants/postdoctoral-researcher-in-time-resolved-crystallography-1357683.kjsp?RH=1135797159702996 ] . We advice to contact Elke De Zitter (elke.de-zit...@ibs.fr) to obtain more information about the postdoctoral position and application procedure. All the best, Elke Elke De Zitter Institut de Biologie Structurale - IBS group DYNAMOP 71 avenue des Martyrs 38044 Grenoble Cedex 9, France +33 4 57 42 86 56 elke.de-zit...@ibs.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- Date:Fri, 22 Dec 2023 12:11:40 + From:Panneels Valérie Subject: Postdoc opportunity at the PSI of Switzerland. Dear Colleagues, The Laboratory of Biomolecular Research at the Paul Scherrer Institute (PSI), Switzerland, is advertising for a Postdoc position from the NanoArgovia Programm of the Swiss Nanoscience Institute (SNI). This project is granted for one year and extendable to 2 years. The project is based on Electron Diffraction Crystallography on proteins either photosensitive or involved in pharma applications. The PSI is the largest research institute for natural and engineering sciences in Switzerland (https://www.psi.ch/en) and hosts a synchrotron, the X-ray free electron laser SwissFEL and an electron microscopy facility (https://www.psi.ch/en/emf). The BIO division together with our PSI detector group has developed a unique instrument for electron diffraction with a dedicated ED-detector based on PSI detector technology. Our laboratory (please consult https://www.psi.ch/en/lbr) is focused on studyi
[ccp4bb] Coot and Pandda questions
Good morning (French time…) Two unrelated questions… Using Coot, I would like to define some key binding… How can I find the command that is actually issued from an option in the « calculate » menu ? I would like to define a key binding for the function « NCS Tools -> Update NCS ghost using local match ». About Pandda… Nick Pearce helped me about my previous request about pandda… I am now able to run pandda_analysis, but pandda_inspect still issues an error. I would therefore like to install ccp4 7.0 instead of the ccp4 7.1 (Pandda web site states that 7.0 should work). Is it possible to find old CCP4 versions to download and install (I am working with MacOS)? Thanks for your help, Laurent Laurent Maveyraud Professor of Biophysics | University of Toulouse | Structural Biophysics Team Doctoral School Biology - Health - Biotechnologies +33 5 61 17 54 35 | +33 6 46 04 21 11 | laurent.maveyr...@ipbs.fr <mailto:laurent.maveyr...@ipbs.fr> | L. Maveyraud <https://fr.linkedin.com/in/laurent-maveyraud-8b394a5> | L. Maveyraud <https://orcid.org/-0003-4610-8319> UMR5089 | CNRS - UT3 | 205 Route de Narbonne BP 64182 - 31077 Toulouse Cedex 4 ipbs.fr <https://www.ipbs.fr/>| Team Website <https://www.ipbs.fr/structural-biophysics>| pict.ipbs.fr <https://cribligand.ipbs.fr/> @IpbsToulouse <https://twitter.com/IpbsToulouse> ipbs.cnrs <https://www.facebook.com/IPBS.CNRS/> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Running Pandda with CCP4 7.1 ?
Hi, I would like to run pandda on some datasets… The pandda website says that pandda currently does not work with ccp4 7.1, and that an update is expected. Instead, pandda should be used with CCP4 7.0.72. What is the current status of pandda with CCP4 7.1 ? If I need to use CCP4 7.0, where can I download it (MacOS )? Thanks for your help ! Laurent Laurent Maveyraud Professor of Biophysics | University of Toulouse | Structural Biophysics Team Doctoral School Biology - Health - Biotechnologies +33 5 61 17 54 35 | +33 6 46 04 21 11 | laurent.maveyr...@ipbs.fr <mailto:laurent.maveyr...@ipbs.fr> | L. Maveyraud <https://fr.linkedin.com/in/laurent-maveyraud-8b394a5> | L. Maveyraud <https://orcid.org/-0003-4610-8319> UMR5089 | CNRS - UT3 | 205 Route de Narbonne BP 64182 - 31077 Toulouse Cedex 4 ipbs.fr <https://www.ipbs.fr/>| Team Website <https://www.ipbs.fr/structural-biophysics>| pict.ipbs.fr <https://cribligand.ipbs.fr/> @IpbsToulouse <https://twitter.com/IpbsToulouse> ipbs.cnrs <https://www.facebook.com/IPBS.CNRS/> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Postdoctoral position, Institut Européen de Chimie et Biologie, Bordeaux, France
Dear all, A One 2-year postdoctoral position funded by the ANR (Agence Nationale pour la Recherche) is available in the « structure and function of bacterial nanomachines » group at Institut Européen de Chimie et Biologie in Pessac (near Bordeaux). The project is dedicated to the study of protein complexes involved in the assembly of the /Helicobacter pylori/type IV secretion system. The selected candidate will be in charge in the purification and structure determination of the complexes by X-ray crystallography or Cryo-EM in collaboration with the group of Dr. Laurent Terradot (IBCP, Lyon, France). She/he will use a wide range of approaches /in vitro/ and /in vivo/ (including molecular biology, biochemistry, microbiology and structural biology techniques such as single particule CryoEM and Cryo-tomography). Interested candidates should have recently obtained a Ph.D. in molecular/structural biology and should have relevant research publications in this field. Candidates should be self-motivated and have recently obtained a PhD degree in Biochemistry, Structural Biology or related disciplines. Candidates should also have practical knowledge of protein biochemistry and experience in protein complex purification and characterization. Experience in X-ray or Cryo-EM data processing would be an asset but is not mandatory The position will be available in 2021. The starting date will be decided in agreement with the selected candidate, preferably during the first trimester of 2022. *Contact*: *Applications in the form of a CV, publication list, a summary of research activities (2 pages max) and contact details of two referees, should be sent by Email to Rémi Fronzes (**r.fron...@iecb.u-bordeaux.fr)* <mailto:r.fron...@iecb.u-bordeaux.fr)>*or Laurent Terradot (laurent.terra...@ibcp.fr) * *Selected candidates will be individually interviewed and a final decision will be made before the end of January 2022.* -- Laurent Terradot Director of Research CNRS Principal Investigator lab web page:http://perso.ibcp.fr/laurent.terradot/terradot_lab/Terradot_Lab.html Structural Biology of Bacterial Macromolecular Complexes Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS-Université Lyon 1 7 passage du vercors, 69007 Lyon Cedex, France Cell Phone +33(0)6 33 69 73 14 Phone +33(0)4 72 72 26 52 Fax +33(0)4 72 72 26 04 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] 48 months PhD fellowship in Structural Microbiology available in Lyon, France
Dear ccp4bb, dear colleagues, A 4-years phD fellowship for (and only for) a Chinese citizen is available in my laboratory in the frame of the France-China collaboration agreement with the University of Lyon. The PhD project is to study the structure and function of the type IV secretion system of Helicobacter pylori (See Bergé et al., 2017; Koelblen et al., 2017). Protein and complexes involved in substrate translocation will be purified and their structures will be determined by X-ray crystallography and/or Cryo-EM. (detailed here https://www.universite-lyon.fr/medias/fichier/ediss-l-terradot-en-_1608113877579-pdf?ID_FICHE=88505) The applicant must hold a Master's degree in Biochemistry and have proven experience in protein purification. The laboratory languages are english and french and the candidate must be fluent in one of them. To apply, send a cover letter, 1-2 reference letters and a detailed CV to Dr. Laurent Terradot (laurent.terra...@ibcp.fr) Details on how to apply can be found here and the deadline for application is February the 10th https://www.universite-lyon.fr/research/phd/phd-csc/csc-phd-scholarships-candidates-applying-to-a-phd-program-at-the-universite-de-lyon-10386.kjsp?RH=1543929774954 -- Laurent Terradot Director of Research CNRS Principal Investigator lab web page: http://perso.ibcp.fr/laurent.terradot/terradot_lab/Terradot_Lab.html Structural Biology of Bacterial Macromolecular Complexes IBCP, UMR 5086 CNRS-Université Lyon 1 7 passage du vercors, F-69367, France Cell Phone +33(0)6 33 69 73 14 Phone +33(0)4 72 72 26 52 Fax +33(0)4 72 72 26 04 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] adding external planar restraint in refmac5
Dear CCP4 users, I am currently refinining an enzyme structure obtained in the presence of a substrate analog : the catalytic serine is acylated and form an ester bond with the ligand. I have added a LINK record in the PDB file to specify the newly created covalent bond between OG atom of Serine and C1 atom of the ligand. I would also like to restraint the ester linkage in a plane (atom OG of Ser623 and atoms O1, C1 and CA or residue 901, both in chain A) I am trying to use the external restraint keyword in refmac (the documentation clearly indicates the syntax in case of a dihedral external restraint and only says that if can also be used for planar restraint). external planar first chain A residue 623 atom OG next chain A residue 901 atom CA next chain A residue 901 atom C1 next chain A residue 901 atom O1 value 0 sigma 10 In the refmac logfile there are no error messages, but this specific command line is not echoed, although all other are. However, it seems to be red and checked by refmac, as introducing a wrong keyword (eternal instead of external) generated an error message. However, the ester linkage is not planar in the refined PDB when viewed with coot. So, is my syntax correct ? Should I keep the value keyword (as it is likely not used I the case of a plane restraint) ? Sigma is set to 10… As far as I understood, this means that this specific plane restraint will be 10 times weaker than the normal plane restraint defined in the standard dictionnaire… is that correct ? Any clues will be more than welcome ! Have a nice day, Laurent Laurent Maveyraud Prof. University of Toulouse www.ipbs.fr | cribligand.ipbs.fr IPBS-Toulouse | CNRS-Université Toulouse III-Paul Sabatier 205 Route de Narbonne, BP 64182, 31077 Toulouse Cedex 4 +33 5 61 17 54 35 | +33 6 46 04 21 11 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Post-doctoral position in IBCP, Lyon- France
Dear all, *A 2 years postdoctoral position funded by the Agence National de la Recherche (ANR) *is available in the group of Dr. Laurent Terradot (@LaurentTerradot ) in the Unit Molecular Microbiology and Structural Biochemistry (MMSB) of the Institut de Biologie et Chimie des Protéines (IBCP, CNRS-University of Lyon), Lyon, France. We are interested in structure function of protein-protein complexes involved in Helicobacter pylori pathogenesis. This bacterium is a major human pathogen that can cause human diseases such as ulcers and gastric cancers. The position is dedicated to the understanding of Helicobacter pylori Type IV secretion system by the determination of several protein-protein complexes by X-ray crystallography or Cryo-EM. Preliminary data are already available for several protein samples. For more information on the project see Koelblen et al., 2017; Bergé and Terradot, 2017; Bergé, Wakmsan and Terradot, 2017, Bats et al., 2018; Zhao et al., 2019. The IBCP (www.ibcp.fr) is well equipped for cell biology, molecular biology and biochemistry and Structural Biology and belongs to a larger campus (Lyon Biopole; Center for Infectiology), giving access to state-of-the-art core facilities in areas. The group has regular access to synchrotron beam time and Cryo-EM. Lyon is a vibrant, historical French city and is a world-excellence center in infectiology. Working language of the laboratory is English. We are looking for enthusiastic and self-motivated individuals with a strong background in protein purification and Structural biology. Experience in the study of complexes would be a plus. Knowledge in Macromolecular Crystallography and/or Cryo-EM would be considered an advantage but is not mandatory. Proposed starting date: *February 2020 * Salary is according to the CNRS french guidelines and should be between 2500-3200 euros gross monthly according to experience. *Interested candidates must apply online*on the CNRS website: https://emploi.cnrs.fr/Offres.aspx with a CV, reference letter(s) and a short summary of your experience/motivation ** Laurent Terradot -- Laurent Terradot Director of Research CNRS Principal Investigator lab web page: http://perso.ibcp.fr/laurent.terradot/terradot_lab/Terradot_Lab.html Structural Biology of Bacterial Macromolecular Complexes IBCP, UMR 5086 CNRS-Université Lyon 1 7 passage du vercors, F-69367, France Cell Phone +33(0)6 33 69 73 14 Phone +33(0)4 72 72 26 52 Fax +33(0)4 72 72 26 04 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] looking for promotif...
Dear all, we are currently trying to pick up the trail of the PROMOTIF program for which we can't find a link that works properly. Does anybody know where I can find it ? thanks for your help, laurent -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr P I C T --- Plateforme Intégrée de Criblage de Toulouse Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 Département BiologieStructurale et Biophysique http://cribligand.ipbs.fr http://www.ipbs.fr 205 route de Narbonne 31077 TOULOUSE Cedex FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
Re: [ccp4bb] P3212--1's in Space Group Names?
Hi, this is explained in details in table 2.2.4.1 of vol A of International Tables of Crystallography (p 18 in my edition). For trigonal/hexagonal, the primary direction is along c, along the 3-fold (6-fold axis). It's the same in tetragonal (obviously for the 4-fold axis !).. The secondary directions for trigonal/hexagonal are [100], the a vector, [010], the b vector, and [-1-10] the diagonal direction between -a and -b vectors (and therefore of between the a and b vectors). In tetragonal, the secondary directions are only [100], a, and [010], b. The tertiary direction for trigonal/hexagonal are [120] and [-2-10] which are directions perpendicular to a and to b, respectively, and [1-10]. None of these directions are the diagonal of a and b vectors. In tetragonal, the tertiary directions are [110], the diagonal of the a and b vectors, and [1-10], the diagonal of the a and -b vectors. laurent Le 18/02/2015 17:04, Kay Diederichs a écrit : Hmm, placeholder for me does not seem to emphasize enough the role that this number plays in the space group names. My understanding (but I fail to remember where I read this ...) is that the first number is the order of the rotation (i.e. 6,4,3,2 or 1) of the unique unit cell axis (often the one with the highest symmetry), the second number is the rotation order of a secondary axis, and the third number gives the rotation order of a tertiary axis - which is the third axis in the orthorhombic system, but a diagonal at least in the trigonal and tetragonal (and I think cubic) systems. This makes it clear that each (baseline) letter in the spacegroup name has its specific role, and tells you about the order of the rotation axis. On top of that comes the screw axis information which is much easier to read when using subscripts. But obviously the naming scheme was chosen such that even if screw axes are not indicated with subscripts, the resulting names are unambiguous. best, Kay -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr P I C T --- Plateforme Intégrée de Criblage de Toulouse Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 Département BiologieStructurale et Biophysique http://cribligand.ipbs.fr http://www.ipbs.fr 205 route de Narbonne 31077 TOULOUSE Cedex FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
[ccp4bb] problems with wincoot 8.1 on windows 7 with multiple desktop
Dear CCP4 users, I just installed the latest CCP4 / wincoot on my windows 7 machine. This machine runs also the dexpot software in order to have multiples desktop. Wincoot runs fine as long as I don't switch to an other desktop. If I do and come back to the desktop where wincoot is displayed, I get a blank wincoot windows : menus and buttons are still available, but the graphic window is grey... Wincoot appears however to still run normally (I can see that hitting the barspace changes to the next residue, as indicated by the text as the bottom of the windows) but the graphic remains blank... Things were fine with wincoot 0.7.2... any ideas ?? thanks laurent -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr P I C T --- Plateforme Intégrée de Criblage de Toulouse Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 Département BiologieStructurale et Biophysique http://cribligand.ipbs.fr http://www.ipbs.fr 205 route de Narbonne 31077 TOULOUSE Cedex FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
Re: [ccp4bb] Question on Refmac5
Dear Dialing, have you any specific reasons to believe that the crated PDB file does not correspond to the refined model ? This could be easily checked by comparing the statistics written in the header of the PDB file and those at the end of the refmac logfile. If they do not differ, then your PDB file should be correct. Laurent Le 06/01/2015 11:46, Tim Gruene a écrit : Dear Dialing, unless this has changed recently, in my experience refmac5 writes the PDB and MTZ file only at the end of refinement, not intermediately. Have you ruled out this is an issue with your operating system or file system setup? Maybe the timestamp is messed up e.g. through an NFS system? What is your operating system, what file system are you running the refinement on? Regards, Tim On 01/06/2015 04:16 AM, Dialing Pretty wrote: I am talking the creating date. For my situation, once the PDB file and mtz file were created at around 6:00 pm, with the progression of the refinement and completed at 8:00 pm, the date shown in the directory folder is always 6:00 pm. After 8:00 pm when the refinement finished, I check the property of the PDB file and MTZ file, I find the modify time (should be by Refmac5) is only several seconds after the created time and the visited time, and the created time and the visited time are same. Clearly I cannot get the expected PDB file and the MTZ file after 2 hours refinement. Is any bug in my CCP4? Or there is something I do not understand? Dialing On Tuesday, 6 January 2015, 10:10, CHAVAS Leonard ccp4hnaa...@gmail.com wrote: Dear Dialing are you talking about the 'creating date' or the 'modified date'? Leo On Jan 6, 2015, at 2:55 AM, Dialing Pretty 03f1d08ed29c-dmarc-requ...@jiscmail.ac.uk wrote: Dear All, When I run Refmac, it would produce a refined PDB file and mtz file. My question is, if I started the refinement at 6:00 pm and completed at 8:00 pm, I find the refined PDB file and mtz file were created in the target directory at perhaps 6:30 pm. I think from 6:30 pm the created PDB file and mtz file in the target directory would be automatically updated to 8: 00 pm when the refinement finished, am I right? Dialing -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr P I C T --- Plateforme Intégrée de Criblage de Toulouse Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 Département BiologieStructurale et Biophysique http://cribligand.ipbs.fr http://www.ipbs.fr 205 route de Narbonne 31077 TOULOUSE Cedex FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
[ccp4bb] depositing PDB files from refmac
Good morning CCP4 list I am trying to deposit structures refined with refmac (latest version 5.8.0049, windows seven), and I have two issues raised at the validation step : 1) there are chain breaks in my protein (for disordered loops). Refmac adds a LINKR record for the description of the break. These are rejected at the validatin step : they are not recognized as valid. If I remove them (and add the TER record at the end of each chain that refmac keeps removing), I have a warning since residues 154 and 160 are not properly linked I didn't find anything for the appropriate description of chain breaks in the descriptin of the PDB format. 2) the R/Rfactor computed by the validation server (either sfcheck or refmac) are quite high : my refinement run gives me 0.188/0.220 when the PDB gives 0.24/0.264 (sfcheck) or 0.20/0.23 (refmac). And, indeed, if I feed to refmac the refined structure it has just produced, I get more or less the same R/Rfree than the PDB. I do use TLS refinement (1 TLS group per chain, 6 chains with NCS), and input them as fixed TLS parameters. TLS contributin is added to Bfactors and ANISOU lines). How could I handle this properly ? Or should I just ignore this ? thaks ! laurent -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr P I C T --- Plateforme Intégrée de Criblage de Toulouse Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 Département BiologieStructurale et Biophysique http://cribligand.ipbs.fr http://www.ipbs.fr 205 route de Narbonne 31077 TOULOUSE Cedex FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
[ccp4bb] Post-doctoral position in Lyon, France
Post-doctoral position in Structural Biology of Bacterial Pathogenesis at the IBCP (Lyon, France) ** *A FINOVI (http://www.finovi.org) funded postdoctoral position *is available immediately in the group of Laurent Terradot at the Institut de Biologie et Chimie des Protéines (IBCP), Lyon, (http://www.ibcp.fr). We are interested in the structure/function of protein complexes involved in bacterial pathogenesis. The funded position will aim to solve the structures of type IV secretion system effectors and understand their mode(s) of action (see Tosi /et al/., Febs L, 2009; Jimenez-Soto /et al/., PloS Pathogens, 2009; Kaplan-Türköz et al., PNAS, 2012). The project is a collaboration between our laboratory and team of P. Doublet at the University of Lyon 1. The IBCP is well equipped for Molecular Biology, Biochemistry, Bioinformatics and Structural Biology and belongs to a larger campus (UMS3444/US8, Lyon Biopole; Center for Infectiology), giving access to state-of-the-art core facilities, including crystallogenesis and biophysics platforms. The group has regular access to synchrotron beam time and is ideally located one hour from the European Synchrotron ESRF. Lyon is a vibrant, historical French city and is a world-excellence center in Infectiology. We are looking for enthusiastic and self-motivated individuals with a strong background in X-ray crystallography, model building and refinement. Successful experience in protein purification for structural studies is required. Experience in protein-protein interactions (Biacore, ITC) and/or study of large complexes would be a plus. Working language of the laboratory is English. Starting date: *As soon as possible*. Salary is according to the CNRS french guidelines. Please send a cover letter, your CV and reference letters as a single PDF file to: *laurent.terra...@ibcp.fr mailto:laurent.terra...@ibcp.fr* ** *Address:* ** *Laurent Terradot* ** /Institut de Biologie et Chimie des Protéines/ /ATIP-CNRS Group Structural Biology of Bacterial Macromolecular Complexes/ /UMR 5086 CNRS Université de Lyon/ /7, passage du Vercors/ /69367 Lyon cedex 07 FRANCE/ //tel: +33 (0) 472 72 2652 Fax: +33 (0) 472 72 2604 -- Laurent Terradot ATIP-Avenir Group Leader Structural Biology of Bacterial Macromolecular Complexes Université Lyon 1, Univ Lyon, France; CNRS, UMR 5086 ; Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP 7 passage du vercors, F-69367, France Phone +33(0)4 72 72 26 52 Fax +33(0)4 72 72 26 04
Re: [ccp4bb] Nvidia 3D Vision 2 - Centos5 - Coot
Hi, on a Mandriva system, we had it working adding those two lines in the xorg.conf file, in the Section Screen : Option Stereo 10 Option Stereo AllowDFPStereo 1 The first line is mandatory with a LCD monitor. I have no idea what the second line means.. but it works with coot. hope this helps laurent Le 14/06/2012 13:19, S. Thiyagarajan a écrit : Dear CCP4 users Has anybody successfully configured NVIDIA 3D VISION-2 kit in CentOS-5.x and used COOT hardware stereo. I am currently having Quadro 4000 graphics card and a 3D compatible Alienware monitor. I could configure these easily in windows but not getting much clues for CentOS-5.x. Please point me to the right pages if this has been discussed already. Thanks for your help regards Thiyaga S. Thiyagarajan Centre of Excellence in Bioinformatics School of Biotechnology Madurai Kamaraj University Madurai - 625021 Ph: +91-9159224881 (cell) -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 PICT -- Plateforme Intégrée de Criblage de Toulouse Département BiologieStructurale et Biophysique BP 64182 - 205 rte de Narbonne - 31077 TOULOUSE FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
Re: [ccp4bb] Nvidia 3D Vision 2 - Centos5 - Coot
In our case, the emitter is indeed connected to the graphic card with the 3 pin mini cable. The cable was included in the box. Le 14/06/2012 14:32, Sabuj Pattanayek a écrit : Do you not need the 3 pin mini din to 2.5mm vesa cable with the 3d vision v2 emitter under linux? I haven't found a model # for this kit that comes with this cable and last I checked nvidia store was out of stock on purchasing these cables separately, so we still purchase the v1 kits. On Thu, Jun 14, 2012 at 6:55 AM, Laurent Maveyraud laurent.maveyr...@ipbs.fr wrote: Hi, on a Mandriva system, we had it working adding those two lines in the xorg.conf file, in the Section Screen : Option Stereo 10 Option Stereo AllowDFPStereo 1 The first line is mandatory with a LCD monitor. I have no idea what the second line means.. but it works with coot. hope this helps laurent Le 14/06/2012 13:19, S. Thiyagarajan a écrit : Dear CCP4 users Has anybody successfully configured NVIDIA 3D VISION-2 kit in CentOS-5.x and used COOT hardware stereo. I am currently having Quadro 4000 graphics card and a 3D compatible Alienware monitor. I could configure these easily in windows but not getting much clues for CentOS-5.x. Please point me to the right pages if this has been discussed already. Thanks for your help regards Thiyaga S. Thiyagarajan Centre of Excellence in Bioinformatics School of Biotechnology Madurai Kamaraj University Madurai - 625021 Ph: +91-9159224881 (cell) -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 PICT -- Plateforme Intégrée de Criblage de Toulouse Département BiologieStructurale et Biophysique BP 64182 - 205 rte de Narbonne - 31077 TOULOUSE FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 -- -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 PICT -- Plateforme Intégrée de Criblage de Toulouse Département BiologieStructurale et Biophysique BP 64182 - 205 rte de Narbonne - 31077 TOULOUSE FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
Re: [ccp4bb] P321 space group reindex problem
Hi, it is therefore likely that your spacegroup is really P321... hopefully, your data set is not twinned, did you check that ? You are left with 2 possible indexing schemes, as already mentionned. Chek scaling derivative / native scaling for each indexation of the derivative : the lowest Rfactor will likely indicate the right one. It appears that you end up with Rfactor of about 29 %, which suggest that your derivatives are not isomorphous to your native dataset. How do cell parameters compare for each data set ? Check also how the Rfactor varies with resolution, you might still have usefull phasing info at low resolution. hope this helps laurent Le 30/05/2012 07:50, Qixu Cai a écrit : At first, I processed the data at P3 space group. But after phenix.xtriage analysis, the Xtriage told me the space group must be P321, so I used P321 to process my data, and got an acceptable Rmerge. Qixu Cai 2012/5/29 Phil Evans p...@mrc-lmb.cam.ac.uk mailto:p...@mrc-lmb.cam.ac.uk How do you know the point group is 321? What does Pointless tell you if you put in the unmerged data? Despite some of the things said earlier (by me!), the possible indexing schemes in 321 are h,k,l and -h,-k,l If that doesn't work, it suggests that the point group is a lower symmetry eg P3 Phil On 29 May 2012, at 16:29, Qixu Cai wrote: Dear all, thank you for your help. I think I must describe my case in detail. I collected a native dataset and two heavy atom derivant datasets （in fact, i don not know whether these two kind of heavy atom have soked into the crystal, i just collect the data to check it）. i processed all of three datasets with automar, and merged them by CAD. I used scaleit to get the Rfactor between datasets and got a strange result. the R factor between derivant1 and native is 26% and the R factor between derivant2 and native is 59%! so I think it may be the problem of index （space group is P321）. so i exchange the h and k of derivant2 by the some awk script and merged to native data by CAD. After scaleit analysis, I got the R factor 29% between derivant2 and native. Here is my questions, 1, at my case, is that right to invert the hand? is that the special problem of the P3 or p321 space group? 2, I have carryed out some suggestion of yours, such as use pointless （use native data as reference for derivant2 reindex）, or reindex the derivant2 dataset by （k, h, -l）, and I always got the high R factor 59% between derivant2 and native. Any suggestion? thanks a lot! Qixu Cai 在 2012-5-29，下午10:36，Laurent Maveyraud laurent.maveyr...@ipbs.fr mailto:laurent.maveyr...@ipbs.fr 写道： Hi... and apologies ! I was a little quick in my answer... in P321, h k l and -h -k l are valid indexing schemes... It is in P3 that you can have h k l and k h -l as Ian and Phil agreed on the BB ! sorry, laurent Hi, you might have several possible spacegroups possible when processing your data (at the indexation step). These will be based on the metrics of your cell (vector length and angles). If you happen to have something like a = b, and alpha=beta90° and gamma=120°, then it is likely that your crystal is trigonal or hexagonal. You will have to wait until the scaling step (or pointless after integration) in order to decide which spacegroup is the right one, based on the symmetry operations in your dataset and on systematic absences. There you have to choose between P3, P31, P32, P312, P321 in trigonal. When comparing two datasets from trigonal crystals, even for identical crystals and hence identical spacegroups, you have different ways to index your dataset... In P321, one dataset might be indexed one way (eg. h k l), the other might be index the other way (k h -l). When you compared this two dataset, they will appear to be different, because both indexing schemes, although valid, are not equivalent. Take one reflection; e.g. 3 2 1 from your crystal A. The very same reflection will be indexed 2 3 -1 for your crystal B, and the one indexed 3 2 1 for crytal B will not be equivalent to the 3 2 1 reflection from crystal A. If you try to merge your two datasets, you will have huge Rmerge, because you are trying to average non equivalent reflections. You will have to ensure that the same indexing scheme is used for both datasets, eg reindex B using the reindex k h -l command in reindex, before being able to merge A and B. hope this helps... please feel free to as if I am not clear... best regards laurent Le 29/05/2012 16:03, Qixu Cai a écrit
Re: [ccp4bb] MAD data process problem
Hi, you are right, the peak dataset corresponds to the highest f'' value. However, this does not mean that f'' is null for the other wavelengthes... you still have significant anomalous signal at the edge and for the high energy remote wavelength... this will help your phasing, so use it ! As Tim mentionned it : process all wavelength with anomalous switched on ! laurent Le 30/05/2012 07:59, Qixu Cai a écrit : Thank you very much for your reply. In my own understanding, We collect the peak dataset, because of the large F'', and we can get strong anomalous signal. We collect the edge dataset, because of the large F', and combined with the remote dataset, we can use the method just like SIR to get some information about the phase. so I think for peak dataset, anomalous processing is necessary, and for edge and remote dataset, anomalous processing is not necessary. Is my understanding correct? Thank you very much for your help. Best wish, Qixu Cai 2012/5/29 Tim Gruene t...@shelx.uni-ac.gwdg.de mailto:t...@shelx.uni-ac.gwdg.de -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Qixu Cai, MAD phasing is based on the comparison of Bijvoet-pairs, i.e. I(hkl) with I(-h-k-l), both within one data set and between data sets. Therefore you might get better results if your integration program does not assume Friedel-pairs to have identical intensities, even though the difference is probably only marginal (integration programs do not merge data). So it is safest click on 'anomalous' for all data sets involved . Tim On 05/29/12 11:11, Qixu Cai wrote: Dear all, Sorry for the question from MAD beginner. When we process the MAD datasets, including the peak-data, edge-data and remote-data, which datasets need to be process with anomalous? I know peak-data obviously need data processing with anomalous, but what about edge-data and remote-data when we want to use MAD method? Thank you very much! Best wishes, Qixu Cai - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPxJfaUxlJ7aRr7hoRAm3EAKCKkyvT8z0wg6MFjflkHkiq8RR5GQCgyvF3 lOIOLypSzCcN3N6OR/3NcC8= =m6ax -END PGP SIGNATURE- -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 PICT -- Plateforme Intégrée de Criblage de Toulouse Département BiologieStructurale et Biophysique BP 64182 - 205 rte de Narbonne - 31077 TOULOUSE FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
Re: [ccp4bb] P321 space group reindex problem
Hi, Le 30/05/2012 08:29, Qixu Cai a écrit : Thank you for your remind of the twin problem. It is always a pleasure to be helpful ;-) By the way, you stated the spacegoup is P321... did you check systematic absences ? could it be P3121 / P3221 ? I checked all of the datasets by Xtriage, and found that the native is not twinned, but the derivant1 and derivant2 are both twinned. So is the Rfactor between derivants and native useful for the judgement of the success of the heavy atom soaking? Well, the unhelpful answer will be : it depends what is your twin fraction ? how does the scaling derivative/native perfom (in details... not only global Rfactors) Did you try to calculate Patterson maps (isomorphous and anomalous) ? I would try to find a good MIR tutorial (CCP4 website might be a good place to look at, but have a look at phenix website...), and try to adapt it to your specific case... good luck ! laurent Thanks. Best wishes, Qixu Cai 2012/5/30 Laurent Maveyraud laurent.maveyr...@ipbs.fr mailto:laurent.maveyr...@ipbs.fr Hi, it is therefore likely that your spacegroup is really P321... hopefully, your data set is not twinned, did you check that ? You are left with 2 possible indexing schemes, as already mentionned. Chek scaling derivative / native scaling for each indexation of the derivative : the lowest Rfactor will likely indicate the right one. It appears that you end up with Rfactor of about 29 %, which suggest that your derivatives are not isomorphous to your native dataset. How do cell parameters compare for each data set ? Check also how the Rfactor varies with resolution, you might still have usefull phasing info at low resolution. hope this helps laurent Le 30/05/2012 07:50, Qixu Cai a écrit : At first, I processed the data at P3 space group. But after phenix.xtriage analysis, the Xtriage told me the space group must be P321, so I used P321 to process my data, and got an acceptable Rmerge. Qixu Cai 2012/5/29 Phil Evans p...@mrc-lmb.cam.ac.uk mailto:p...@mrc-lmb.cam.ac.uk mailto:p...@mrc-lmb.cam.ac.uk mailto:p...@mrc-lmb.cam.ac.uk__ How do you know the point group is 321? What does Pointless tell you if you put in the unmerged data? Despite some of the things said earlier (by me!), the possible indexing schemes in 321 are h,k,l and -h,-k,l If that doesn't work, it suggests that the point group is a lower symmetry eg P3 Phil On 29 May 2012, at 16:29, Qixu Cai wrote: Dear all, thank you for your help. I think I must describe my case in detail. I collected a native dataset and two heavy atom derivant datasets （in fact, i don not know whether these two kind of heavy atom have soked into the crystal, i just collect the data to check it）. i processed all of three datasets with automar, and merged them by CAD. I used scaleit to get the Rfactor between datasets and got a strange result. the R factor between derivant1 and native is 26% and the R factor between derivant2 and native is 59%! so I think it may be the problem of index （space group is P321）. so i exchange the h and k of derivant2 by the some awk script and merged to native data by CAD. After scaleit analysis, I got the R factor 29% between derivant2 and native. Here is my questions, 1, at my case, is that right to invert the hand? is that the special problem of the P3 or p321 space group? 2, I have carryed out some suggestion of yours, such as use pointless （use native data as reference for derivant2 reindex）, or reindex the derivant2 dataset by （k, h, -l）, and I always got the high R factor 59% between derivant2 and native. Any suggestion? thanks a lot! Qixu Cai 在 2012-5-29，下午10:36，Laurent Maveyraud laurent.maveyr...@ipbs.fr mailto:laurent.maveyr...@ipbs.fr mailto:laurent.maveyraud@__ipbs.fr mailto:laurent.maveyr...@ipbs.fr 写道： Hi... and apologies ! I was a little quick in my answer... in P321, h k l and -h -k l are valid indexing schemes... It is in P3 that you can have h k l and k h -l as Ian and Phil agreed on the BB ! sorry, laurent Hi, you might have several possible spacegroups possible when processing your data (at the indexation step
Re: [ccp4bb] MAD data process problem
Hi, when processing MAD data, all wavelength should be processed without enforcing the Friedel's law... If you look at your fluorescence spectrum, you will see that you have anomalous signal for the peak (obviously) for the high energy remote and even forh the inflexion point. For example, in the case of Se-MAD : peak : f'=-6, f''-8 inflexion : f'=-11, f''= 4 high remote : f'= -4, f''= 4 the low energy remote is the one with the weakest anamalous signal, close to 0 in the case of Se... hope this helps laurent Le 29/05/2012 11:11, Qixu Cai a écrit : Dear all, Sorry for the question from MAD beginner. When we process the MAD datasets, including the peak-data, edge-data and remote-data, which datasets need to be process with anomalous? I know peak-data obviously need data processing with anomalous, but what about edge-data and remote-data when we want to use MAD method? Thank you very much! Best wishes, Qixu Cai -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 PICT -- Plateforme Intégrée de Criblage de Toulouse Département BiologieStructurale et Biophysique BP 64182 - 205 rte de Narbonne - 31077 TOULOUSE FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
Re: [ccp4bb] Restrained refinement problem
Hi, did you check in the refmac logfile that the cif file created at the first step was actually read ? If it is, you will have to carefully check the cif file and you ligand structure : 1) is the ligand structure included in the PDB at the fisrt step complete ?? Maybe you included only a partial lignad because of weak density... when you add other atoms, they will be missing from the cif file. 2) are all the ligand atoms present in the cif file with correct names ? 3) are the information present in the cif file correct (connectivity, bond order, planar group, chiral center). This will not produce the error you have, but will certainly distort the geometry... hope this helps laurent Le 12/03/2012 06:21, Dipankar Manna a écrit : Dear All, As I am practicing new in the crystallography, I am facing some difficulties in refining the ligand bound structure. Protein I am working with has SG P212121, it’s a dimer. I fitted the ligand on the density with COOT--calculate--Model/Fit/Refine--Rotate/Translate Zone. Then I merged both (protein ligand) the pdb structure and saved the coordinate as .pdb file. By taking this pdb when I am running restrained refinement it was showing: -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 PICT -- Plateforme Intégrée de Criblage de Toulouse Département BiologieStructurale et Biophysique BP 64182 - 205 rte de Narbonne - 31077 TOULOUSE FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
Re: [ccp4bb] High R factor
Hi, it might well be possible that molrep used only lower resolution data (the default cutoff isd 2.5 A, if I remember correctly), when refmac uses all available data in the MTZ file... Check that both steps were performed at the same resolution ! Another possibility is that molrep performed the search in different spacegroups than the one specified in the MTZ file (eg P4 selected during data processing, and molrep checks, P4, P41, P42 and P43). If your solution corresponds to the P41 spacegroup, you have to modify your MTZ file (or use the one produced by molrep)... otherwise refmac will perform the rigid body step in P4 and not P41... This should be indicated in the molrep logfile... check it carefully ! hope this helps. If not please send the logfiles ! Laurent Le 20/02/2012 11:48, Dipankar Manna a écrit : Dear Sir/Madam, I am very new to this CCP4 program. Usually I know that after rigid body refinement the R factor reduces from the R factor what ever we get from Molrep. One of my data is showing some different characteristics. After running Molrep the R factor is showing 38% and score is 64%, but when I run rigid body refinement (Refmac5) the Rfactor is showing 46.07% and Rfree is 46.27. is it possible? Or else what I have to do with this data. Please suggest. Regards Dipankar Manna This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information.If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.Any unauthorized review, use, disclosure, dissemination, forwarding,printing or copying of this email or any action taken in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 PICT -- Plateforme Intégrée de Criblage de Toulouse Département BiologieStructurale et Biophysique BP 64182 - 205 rte de Narbonne - 31077 TOULOUSE FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
Re: [ccp4bb] merge and scale high-res and low-res scans with SCALA
Hi, you first need to be sure that both datasets are indexed the same way (this depends on your spacegroup). During the processing step, you have to give each dataset different batch numbers (directly from imosflm) or you can rebatch them after processing (Data Reduction/Utilities/Sort-Modify-Combine MTZ task in ccp4i). Then you can sort (Data Reduction/Utilities/Sort-Modify-Combine MTZ task in ccp4i) your files in a single run in order to get a merged sorted file that you can feed to scala. hope this helps laurent Le 22/02/2011 22:53, Huiying Li a écrit : I have collected two sets of data, high-res and low-res, with the same crystal and integrated them separately with imosflm. Now I want to merge and scale the two MTZ files with Scala in ccp4i GUI. But I do not know how to input 2 MTZ files through the Scala input GUI window (under Data Reduction module, Scaleand Merge Intensities). Another question on reindexing: The space group for this data set output by imosflm is P21221, which is non-standard. How can I reindex this to P21212, using Sftools or other routine? Thanks for help. Huiying ___ Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 Département BiologieStructurale et Biophysique 205 route de Narbonne 31077 TOULOUSE Cedex FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
[ccp4bb] Post-doctoral position in Structural Biology in Lyon, France
*A post-doctoral position *is available immediately in the group of Laurent Terradot at the Institut de Biologie et Chimie des Protéines (IBCP), Lyon, (http://www.ibcp.fr). We are interested in the structure/function of protein complexes involved in /Helicobacter pylori /pathogenesis. This bacteria is a major pathogen that causes human diseases such as ulcers and gastric cancers. Several projects are available in our laboratory to study 1) virulence factors/receptor interactions (see Tosi /et al/., Febs L, 2009; Angelini /et al/., Febs Journal, 2009; Jimenez-Soto /et al/., PloS Pathogens, 2009) and 2) DNA replication regulation (see Natrajan et al., Mol. Microbiology, 2007; Natrajan et al., PNAS, 2009). Part of the work will be carried out with National and International collaborations. The IBCP is well equipped for Molecular Biology, Biochemistry, Bioinformatics and Structural Biology and belongs to a larger campus (Lyon Biopole; Center for Infectiology), giving access to state-of-the-art core facilities. The group has regular access to synchrotron beam time and is ideally located one hour from the European Synchrotron ESRF. Lyon is a vibrant, historical French city and is a world-excellence center in Infectiology. We are looking for enthusiastic and self-motivated individuals with a strong background in protein purification for structural studies. Experience in protein-protein interactions (Biacore, ITC, etc...) and/or study of large complexes would be a plus. Knowledge in Macromolecular Crystallography would be considered an advantage but is not mandatory as training can be provided. Working language of the laboratory is English. Starting date: *As soon as possible*. Salary is according to the CNRS french guidelines and will depend on experience. Please send a cover letter, your CV and one (or more) reference letter as a single PDF file to: *laurent.terra...@ibcp.fr mailto:laurent.terra...@ibcp.fr * Deadline: May the 1st, 2010. ** * * -- Laurent Terradot Institut de Biologie et Chimie des proteines ATIP-CNRS Group Structural Biology of Bacterial Macromolecular Complexes UMR 5086 CNRS Université de Lyon 7, passage du Vercors 69367 Lyon cedex 07 FRANCE tel: +33 (0) 472 72 2652 Fax: +33 (0) 472 72 2604
[ccp4bb] coot and stereochemistry
Dear list, another question related to stereochemistry, but concerning coot. When using the RSR zone button, which should improve geometry and fit to map, it seems that the geometry is not always improved : some chiral centers can be inverted. The surprising thing is that using the regularize zone afterwards does not correct this, even if the chirality of the center is not set to both, but to positive in the cif dictionnary (ie should define only one possible chirality). Has anybody else notices this behavior ? Is there a way to adjust the weight between geometru and map terms in the RSR option ? thanks for any ideas or advices laurent --- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr Université Paul Sabatier Toulouse III I.P.B.S. UMR 5089 Groupe de Biophysique Structurale Département Mécanismes Moléculaires des Infections Mycobactériennes 205 route de Narbonne 31077 TOULOUSE Cedex FRANCE Tél: +33 (0)561 175 435Fax : +33 (0)561 175 994 --- -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.5.446 / Virus Database: 268.18.14/727 - Release Date: 19/03/2007 11:49
