[ccp4bb] Postdoctoral position in biochemistry with applications in bacteriology (Structure and Biogenesis of the pilus of Streptococcus pneumoniae) in Stockholm, Sweden
Dear group members, I would like to bring to the following opening to your attention: ANNOUNCEMENT TITLE: Postdoctoral position in biochemistry with applications in bacteriology (Structure and Biogenesis of the pilus of Streptococcus pneumoniae) in Stockholm, Sweden DEADLINE FOR APPLICATIONS: 25 October 2007 TYPE OF POSITION: Post-Doc INSTITUTION/DEPARTMENT: Department of Bacteriology, Swedish Institute for Infectious Disease Control, Solna, Sweden AND Center for Infectious Medicine, Department of Medicine, Karolinska University Hospital in Huddinge, Karolinska Institutet CONTACT PERSON: Adnane Achour, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden. e-mail address: [EMAIL PROTECTED], Phone: +46-8-5248 6232, Fax: +46-8-30 42 76, website: http://www.medhs.ki.se/cim/ DESCRIPTION/REQUIREMENTS: A postdoctoral position is available for an enthusiastic individual for a period of two years within the laboratory off Assoc. Prof. Adnane Achour at the Center for Infectious Medicine (CIM), Karolinska Institutet and the adjacent laboratory of Assoc. Prof. Birgitta Henriques-Normark and Prof. Staffan Normark at the Swedish Institute for Infectious Disease Control (SMI) in Stockholm, Sweden. The candidate should be a good team-player. She/he will be responsible for the cloning, production and isolation of proteins that are involved in the structure and the biogenesis of the pilus of Streptococcus pneumoniae. The prime target of this project are sortases A-D as well as the Rrg elements of the pilus. Site directed mutagenesis studies will be combined with a wide array of biochemical and immunological assays, as well as imaging, in order to assess the molecular mechanisms underlying the biogenesis of the pilus. Potential determination of crystallizatio n conditions as well as the determination and interpretation of three-dimensional structures of several proteins that participate in this process may be undertaken by the candidate, either alone or in close collaboration with other members of the research groups. APPLICATION PROCEDURE: The application should include a CV (including in particular any experience relevant to the position announced) as well as the names and contact details of 2 references. The applicants should also submit a list of publications and submitted manuscripts. begin:vcard n:Achour;Adnane fn:Adnane Achour tel;fax:+46-8-30 42 76 tel;work:+46-8-5248 6232 url:http://www.medhs.ki.se/cim/medhs_eng.asp?Id=12&tabell=medhs_english org:Center for Infectious Medicine;Department of Medicine, F59 adr:;;Karolinska University Hospital Huddinge;Stockholm;;141 86;Sweden version:2.1 email;internet:[EMAIL PROTECTED] title:Associate Professor end:vcard
[ccp4bb] New validation program...
Hi! I've just written a new validation program which validates the sequence of a coordinate model to detect register errors caused by extra or missing residues in the chain trace. This was inspired by a recent message from the Richardsons, about something similar in molprobity (I think, I can't find it any more). I realised I already had all the code to do this in buccaneer. However, the approach to sequencing implemented in buccaneer is sufficiently different to anything used elsewhere that it should provide an independent check. It may be run with phases from experimental phasing, or it can calculate its own phases using a side-chain-omit process. In this case it can be used after molecular replacement, or to validate structures in the PDB. The software includes a GUI and auto-installer script, and is available for Linux/x86, Mac/x86 and Mac/ppc. You can download it from here: http://www.ysbl.york.ac.uk/~cowtan/sequins/sequins.html The installer will create a new task in the 'Validation and Depostition' menu, labelled 'Sequence validation'. I've attached a screenshot of the GUI. Below is sample output, showing a case in which there is a 30 residue register shift in the model. Note the '+' and '-' in the modified sequence, and the warning message below. ### ### ### ### CCP4 6.0: csequins version 0.0.1 : 29/08/07## ### User: cowtan Run date: 3/ 9/2007 Run time: 11:44:05 Please reference: Collaborative Computational Project, Number 4. 1994. "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. Copyright 2007 Kevin Cowtan and University of York. All rights reserved. Please reference: Cowtan K. (2006) Acta Cryst. D62, 1002-1011. pdbin-ref /home/cowtan/test/reference-1tqw.pdb mtzin-ref /home/cowtan/test/reference-1tqw.mtz colin-ref-fo/*/*/[FP.F_sigF.F,FP.F_sigF.sigF] colin-ref-hl/*/*/[FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D] mtzin-wrk modified.mtz colin-wrk-fo/*/*/[FP,SIGFP] pdbin-wrk modified.pdb correlation-mode CHAIN: A Original: MKTRADLFAFFDAHGVDHKTLDHPPVFRVEEGLEIKAAMPGGHTKNLFLKAKGQLWLISALGETTIDLKKLHHVIGSGRLASFGPQEMMLETLGVTPGSVTAFGLINDTEKRVRFVLDKALADSDPVNFHPLKNDATTAVSQAGLRRFLAALGVEPMIVDFAAMEVVG Modified: ??TRADLFAFFDAHGVDHKTLDHPPVFRVEEGLEIKAAMPGGHTKNLFLK+AKGQLWLISALGETTIDLKKLHHVIGSGRLASFGP-MMLETLGVTPGSVTAFGLINDTEKRVRFVLDKALADSDPVNFHPLKNDATTAVSQAGLRRFLAALGVEPMIVDFAAMEVV? Confidence: 0.92 WARNING: The supplied data suggests a partial sequence register error. Times: User: 36.9s System:0.1s Elapsed: 0:38 <>
[ccp4bb] Shelx_install_in_ccp4iv6.0.2
Dear All: I am trying to install Shelx C/D/E/ into ccp4i(v6.0.2) using "system administration" tool for task installation. It complains and said: This may not be a valid ccp4i package. How can I intall Shelx into CCP4i? Your help is highly appreciated Regards Xue yuan Pei, Ph.D Department of Biochemistry University of Cambridge Cambridge CB2 1QA U.K
[ccp4bb] Rfree and unaccounted density
Hi all i m solving a structure at 2.2 A using MIR. rt now my Rfree is 30.55% and Rcryst is 28.51%. i have already carried out B factor refinement n water has also been picked up to 2.3 sigma cut off. now i m not able to refine the structure any further. The protein has been purified directly from the source. At this pt of refinement i m able to see lot of unaccounted densities, far bigger to b accounted by water or sugar, as we don't have any information abt the possible molecules that can interact with this protein. . is this unaccounted density be the reason why i m not able to refine the strucure? thanx in advance Vineet Gaur
[ccp4bb] chromatofocusing
I'm forwarding this to the listserve for someone in my lab who is having trouble sending to the list. Replies to the list or directly to Nat Echols ([EMAIL PROTECTED]) are greatly appreciated... Not question about crystallography, but that's the ultimate goal: Has anyone used a custom-made buffer for use with the PBE media sold by GE? I found a bottle of Pharmacia PBE 94 and would like to use it, but if I did I would use it frequently and on a relatively large scale, so I'd rather not pay for the (expensive and proprietary) Polybuffer. Alternately, has anyone done something similar with DEAE/CM media? I've seen references to this (although I suspect the resolution won't be as good), but not very good descriptions. thanks, Nat
