Re: [ccp4bb] Topology diagram
Dear community, Thanks for your helpful answers. @Xavier: Obviously, I knew TopDraw, but as mentioned by Andy “TOPDRAW doesn't interpret a pdb file, it just allows you to draw your own topology diagram.” And I wanted it to be as simple as possible for my biochemist colleague with no access to ccp4 programs. @Andy: The link to generate a PDBsum output, without installing the program, is: https://www.ebi.ac.uk/thornton-srv/databases/pdbsum/Generate.html @Deborah: Thanks for the link of Overprot (https://overprot.ncbr.muni.cz/) @Tom: Pro-origami was exactly what I was looking for, unfortunately the web server is gone (what a pity). Many thanks for the link to actually install the program: (https://sites.google.com/site/alexdstivala/home/pro-origami), which would be extremely useful. Always a pleasure to read and get useful answers from ccp4db, Bests, Lionel 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] Topology diagram
Dear community, A biochemist asks me if I knew a webserver/tool to draw topology diagram of protein from a deposited pdb or part of it, ideally allowing edition (label, colour, etc...). For a better understanding, the topology diagram’s representation is as the picture attached, which I believe is a “key notation” topology diagram. It’s possible to get such diagram from PDBsum but they are fixed (pdf, ps) and I would say (without offence) a bit ugly. After an extensive Google/Ccp4DB/ChatGPT search, for my surprise, I found nothing helpful. It seems that “old” tools like pro-origami are gone/unavailable. I would greatly appreciate any advice on possible website or more specialized program (even if I would do the “webserver” task myself). Best, Lionel 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] Protein crystallographer position available at Sprint Bioscience (Huddinge, Sweden)
Hi, We are recruiting a protein scientist with a passion for protein X-ray crystallography. Apply today if you thrive in an efficient and multi-disciplinary research environment focused on driving innovative drug programs forward. We give you the opportunity to develop both within and outside of your discipline. SPRINT BIOSCIENCE IN SHORT Sprint Bioscience develops small-molecule drugs to fight cancer. With fragment-based drug design methods, advanced technical approaches, and leading specialists, we develop the drugs of the future - from the idea stage to a clinical candidate with the goal set at being "First-in-Class". Our business model is to identify and run drug development projects and license these in the preclinical phase to the global pharmaceutical industry. We choose projects with the greatest technical and commercial potential for success. Sprint Bioscience has had a yearly growth since our start in 2009. Today, we are about 30 committed employees who work closely together in a stimulating environment with cutting-edge methodology and challenging projects. We also collaborate with several academic and industrial partners from all over the world. We are situated in tailored designed premises in Flemingsberg - Huddinge, 20 minutes by train from Stockholm City. ABOUT THE POSITION You will be a member of the Structural Biology team, consisting of scientists with expertise in the different areas related to protein crystallography (recombinant protein expression and purification, crystallogenesis, structure determination). Your main goal will be to develop crystal systems which will allow the generation of high-resolution crystal structures of complexes between proteins from our portfolio and the compounds synthesized by our Medicinal Chemistry team. Because Sprint Bioscience favored hit-to-lead approach is Structure-Based Drug Design, this activity is essential in order to progress our molecules towards a drug-candidate. Depending on your competences, you could also take part in the further structure determination, model refinement and structural analysis steps. We work in efficient and dynamic project teams, which are adaptable and change depending on project priorities. This is a full-time permanent position. YOU WILL MAKE A DIFFERENCE You will bring your expertise into a team of dedicated scientists. You need collaborative skills and to communicate well when supporting parallel projects in a multi-disciplinary environment. Our company language is English. Your main contributions in the field of Structural Biology will be: * Developing stable crystallization protocols suitable for the study by X-ray crystallography of protein-ligand complexes * Applying these protocols to deliver high-resolution diffraction data to support the chemistry programs. Optional: delivering 3D model to chemists and guiding them in their analysis * Sharing responsibilities in term of organization of the structural biology activities (organization of synchrotron sessions, maintenance of the equipment) * Implementing new workflows and new methods for protein crystallography and structural biology in general To be successful in this position you will need: * An extensive experience and expertise in crystallization of soluble proteins and particularly of protein-ligand complexes * A passion for structural biology (protein crystallography) and particularly method development in the different fields of the discipline Having knowledge and experience in the following fields will be considered as benefits: * Structure-based drug-design softwares * Fragment-screening by X-ray crystallography * Structure determination (from data collection to model refinement and analysis) * Protein purification and characterization * Methods in Structural Biology other than X-ray crystallography You will be able to apply to the position by following the link below : https://www.sprintbioscience.com/en/career/available-positions/experienced-scientist-with-a-passion-for-protein-crystallography/ Please, feel free to contact me if you wish more information. Best Wishes / Vänlig hälsning, Lionel Trésaugues ________ Lionel Trésaugues Structural Biology [cid:image001.jpg@01D7CF08.EFE18020] Sprint Bioscience Novum SE 141 57 Huddinge Sweden Tel: +46 (0)8-411 44 55 Mobile: +46 (0)73-075 54 46 www.sprintbioscience.com<http://www.sprintbioscience.com/> Confidentiality Note: This message is intended only for the use of the named recipient(s) and may contain confidential, personal and/or privileged information. If you are not the intended recipient, please delete this message. Any unauthorized use of the information contained in this message is prohibited. To
[ccp4bb] Two postdoctoral positions available in the Department of Medical Biochemistry and Biophysics (Karolinska Institute)
Dear CCP4ers, Sorry for this non-structural biology related jobs announcements, but this will be very helpful if you could spread this message to who might be interested. Two postdoctoral researcher positions are available in the Department of Medical Biochemistry and Biophysics at Karolinska Institutet (Stockholm, Sweden). The work will be done in Pär Nordlund's group who has developed a novel strategy for discovering clinical biochemical biomarkers that bear the potential to improve drug therapies for different cancers. The technology allows for the direct quantification of biochemical changes of activation states of proteins in patient samples using a biophysical principle - the Cellular Thermal Shift Assay (CETSA; Martinez Molina, Science 2013 41;84; Savitski, Science 2014 346:1255784). CETSA measurements of drug target engagement enables direct measurements of the extent to which a drug reaches and binds to its anticipated target in the cancer locus. Target engagement based CETSA biomarkers have the potential to optimize therapy in the individual patient, providing an entirely novel strategy within the emerging field of personalized medicine. The project aims to further develop and validate the CETSA technology in different cell and animal models and patient samples. The successful applicants will work in a dynamic team, developing new implementations of CETSA for application in studies of mechanisms of drug action and resistance development and for discovery of diagnostic markers of therapeutic effect. External collaboration with pharmaceutical companies, research groups, clinicians, biobanks etc will be important in the project. Here are the links to get more details and to apply for the two positions: https://ki.mynetworkglobal.com/en/what:job/jobID:61201/where:4/ https://ki.mynetworkglobal.com/en/what:job/jobID:61205/where:4/ Thank you for your help ! Regards /lionel Lionel Trésaugues | PhD Department of Medical Biochemistry and Biophysics | Karolinska Institutet SE-171 77 Stockholm | Scheeles väg 2 +46 8 524 868 73 | +46 7 042 171 87 lionel.tresaug...@ki.semailto:lionel.tresaug...@ki.se | ki.sehttp://ki.se/ki/jsp/polopoly.jsp;jsessionid=aMdk8ad4iRL6OYOdFn?l=end=130 __ Karolinska Institutet - a medical university
[ccp4bb] How to remove phospholipids bound to a cytoplasmic protein
Dear all, I would like to remove two phospholipids bound to (actually into) a cytoplasmic protein. The protein was expressed in E. coli and the crystal structure revealed the presence of two co-purified phospholipids (most probably DPPE). A web search gave me three methods to remove bound lipids: - 1-butanol liquid–liquid extraction - Lipidex 1000, VI column at 37°C - HIC (aka Hydrophobic Interaction Chromatography) on a Phenyl HP column in presence of 1M ammonium sulphate All are described in Velkov 2008 (http://www.sciencedirect.com/science/article/pii/S1570023208002390). I assume these delipidation methods would also work for phospholipid; and I am more tempting by the last one, the milder one. I would appreciate any comment or practical advice. Best regards, Lionel
Re: [ccp4bb] larger molecular weight shown by analytic ultracentrifugation
Dear Jerry, Just a few comments on your questions. We tried both SV and SE. SV showed an increasing Sw with decreasing concentrations (Sw varied from 6.9, 7.0, 7.2, 7.4 to 7.522). IN addition, the SV experiments showed a single boundary. However, the boundary was a little broader, between 6 and 8.5. SV peaks seem to overlay at lower concentrations with Sw ranging from 7.5 to 7.86. From SV experiments, the calculated Mw is ~125 KD with f/fo equal to 1.2. The monomer of my protein is ~20KD. I am not sure whether 7.86 S would be much faster than a tetramer (~80KD) could possibly sediment. Your data seems to point towards non-ideal behaviour of your protein, more precisely towards repulsive protein-protein interactions. Keep in mind that Mw is an apparent mass that depends on interactions with the solvent and is protein-concentration dependant (in addition to the issue of oligomers). For an example, you could check : Solovyova, A. et al. (2001). Non-ideality by sedimentation velocity of halophilic malate dehydrogenase in complex solvents. Biophys. J. 81:1868-1880. http://dx.doi.org/10.1016/S0006-3495(01)75838-9 I would suggest you to post your questions to the RASMB email list info that is centred on AUC and with very helpful people. Best regards, Lionel
Re: [ccp4bb] Ubuntu 10.10 64-bit and COOT
I install this version of coot: coot-Linux-x86_64-ubuntu-9.04-gtk2 for ubuntu and it works fine Best Lionel Le 07/03/2011 19:35, Eugene Krissinel a écrit : coot has to be installed separately, it is not included in ccp4 6.1.13. It is best to get coot binaries from Paul Emsley directly, just google on coot emsley and look for download pages, then choose ubuntu tarball. Best, Eugene. On 7 Mar 2011, at 18:27, Pranjal Mahanta wrote: Hi, I just installed CCP4-6.1.13 on my ubuntu (10.10) 64 -bit laptop. I can run CCP4i successfully. But when i try to run coot, i get error : No command 'coot' found. Can someone help me to fix the problem? with regards, Pranjal
[ccp4bb] Refmac bref MIXED failed
Hello, When I run Refmac with the mixed iso/anisotripic B-value option (refi bref MIXED), refmac failed with the error message below. My pdb comes from previous refmac runs with anisotropic B values for all atoms (H generated but not written). I just removed from the pdb the ANISOU lines for all water molecules. Refmac with refi bref ANIS (all anisotropic B) works fine (normal termination) with the same input data and pdb - with all ANISOU lines. CCP4Interface 2.0.5 Refmac_5.5.0102 Any comments, help, fix are welcome. Best regards, Lionel ** CGMAT cycle number = 1 . Trying gamma equal0.00 Not converging with gamma equal0.00 Trying gamma equal 5.503E-02 Not converging with gamma equal 5.503E-02 Trying gamma equal 0.1155000 . Not converging with gamma equal2655.967 Trying gamma equal2921.619 Not converging with gamma equal2921.619 Trying gamma equal3213.836 Gamma decreased to3155.393 *** * Information from CCP4Interface script *** The program run with command: /all/programas/ccp4-6.1.2/bin/refmac5 XYZIN /data/refmac8-coot-0Wiso.pdb XYZOUT /tmp/lcocri/21_2_pdb_1.tmp HKLIN /data/4_unique1.mtz HKLOUT /tmp/lcocri/21_3_mtz_1.tmp LIBIN /data/ligand.cif LIBOUT /data/21_lib.cif has failed with error message child killed: SIGABRT *** #CCP4I TERMINATION STATUS 0 child killed: SIGABRT #CCP4I TERMINATION TIME 06 sep 2010 15:28:12 #CCP4I MESSAGE Task failed
Re: [ccp4bb] Refmac bref MIXED failed
Hi Garib, I tried with refmac 5.6 and the same inputs; it worked fine. Thanks, Lionel 2010/9/6 Garib N Murshudov ga...@ysbl.york.ac.uk Could you please try refmac 5.6. I think we have fixed this problem. It is available from: www.ysbl.york.ac.uk/refmac/latest_refmac.html You need to take experimental version (it is now fairly stable) Regards Garib On 6 Sep 2010, at 15:01, Lionel Costenaro wrote: Hello, When I run Refmac with the mixed iso/anisotripic B-value option (refi bref MIXED), refmac failed with the error message below. My pdb comes from previous refmac runs with anisotropic B values for all atoms (H generated but not written). I just removed from the pdb the ANISOU lines for all water molecules. Refmac with refi bref ANIS (all anisotropic B) works fine (normal termination) with the same input data and pdb - with all ANISOU lines. CCP4Interface 2.0.5 Refmac_5.5.0102 Any comments, help, fix are welcome. Best regards, Lionel ** CGMAT cycle number = 1 . Trying gamma equal0.00 Not converging with gamma equal0.00 Trying gamma equal 5.503E-02 Not converging with gamma equal 5.503E-02 Trying gamma equal 0.1155000 . Not converging with gamma equal2655.967 Trying gamma equal2921.619 Not converging with gamma equal2921.619 Trying gamma equal3213.836 Gamma decreased to3155.393 *** * Information from CCP4Interface script *** The program run with command: /all/programas/ccp4-6.1.2/bin/refmac5 XYZIN /data/refmac8-coot-0Wiso.pdb XYZOUT /tmp/lcocri/21_2_pdb_1.tmp HKLIN /data/4_unique1.mtz HKLOUT /tmp/lcocri/21_3_mtz_1.tmp LIBIN /data/ligand.cif LIBOUT /data/21_lib.cif has failed with error message child killed: SIGABRT *** #CCP4I TERMINATION STATUS 0 child killed: SIGABRT #CCP4I TERMINATION TIME 06 sep 2010 15:28:12 #CCP4I MESSAGE Task failed -- ___ Interactions faibles entre protéines en solution Costenaro L. (2010) Editions Universitaires Européennes, ISBN 9786131506048 Livre disponible en francais sur amazon: http://www.amazon.com/s/ref=nb_sb_noss?url=search-alias%3Dapsfield-keywords=ISBN+9786131506048x=0y=0 ___ Dr. Lionel Costenaro Institut de Biologia Molecular de Barcelona - CSIC and Institute for Research in Biomedicine Parc Cientific de Barcelona C/ Baldiri i Reixac 10-12 E-08028 Barcelona, Spain Phone +34 93 403 49 57 Fax +34 93 403 49 79 Emaillionel.costen...@ibmb.csic.es , lionel.costen...@irbbarcelona.org URL www.ibmb.csic.es , www.irbbarcelona.org
[ccp4bb] JLigand and refmac5 merge_monomer bugs
Hello, Just to report two bugs: When adding a link between a ligand and an amino acid with JLigand (0.1 Beta) the cif file may have the following errors (as it was my case): _chem_link_angle.linkId instead of _chem_link_angle.link_id _chem_link_chir.linkId instead of _chem_link_chir.link_id and the data of this block may have additional (unwanted) entries. When merging such a link definition with the ligand definition using the Merge LIBINs tab from refmac5 (ccp4i gui, CCP4Interface 2.0.5), these two definition blocks are just omitted, without any error message (this is the bug). Best regards, Lionel
Re: [ccp4bb] How to reduce free-R factor
Lionel Mourey Institut de Pharmacologie et de Biologie Structurale CNRS - Université de Toulouse 205 route de Narbonne 31077 Toulouse France Tél : 05 61 17 54 36 Mobile : 06 73 50 95 51 Fax : 05 61 17 59 94 E-mail : lionel dot mourey at ipbs dot fr - Message d'origine - De: Pankaj Chauhan pankajimt...@gmail.com Env: vendredi 4 décembre 2009 06:07 À: CCP4BB@JISCMAIL.AC.UK Objet: [ccp4bb] How to reduce free-R factor [Le message original intégral n'est pas inclus]
[ccp4bb] pdb submission with SS bond + alternate and author defined ss
Hello, I have two short questions about submitting a structure to the PDB: 1- How should I submit a structure that has a SS-bond with alternate free cysteines (knowing that the SSBOND record does not support alternate conformation)? 2- How can I keep my author-defined secondary structures during the conversion of the pdb to mmCIF with pdb_extract ? Thanks in advance for your comments, Lionel
Re: [ccp4bb] PERL system call to CCP4
For those who might want to use his package, Emmanuel Courcelle told me that the new URL is : ftp://ftp.toulouse.inra.fr/pub/LIPM/manu/occp4/occp4-pm-1.0.tar.gz It is there since 2002 and will not be moved. Best regards, Lionel On Mon, 14 Jan 2008 16:41:35 -0500, Ezra Peisach [EMAIL PROTECTED] wrote: You may wish to look at the occp4-pm perl package by E. Courcelle and J.P. Samama (formerly available from ftp://ftp.ipbs.fr/pub/occp4 - but this no longer works...) I no longer have a copy but someone might... Ezra [EMAIL PROTECTED] wrote: Dear CCP4 users, I am writing a PERL script to execute a number of CCP4 commands (ncsmask, pdbset, and dm) in succession. I have tried using system call or PIPE command, neither of which work. The ccp4 scripts generated work independently on the command line. Any suggestions? Thank you in advance! =
