[ccp4bb] PostDoc positions
Dear all, I have two PostDoctoral openings in my group. Position #1 - a 3 year PostDoc position in time-resolved crystallography on membrane proteins, based at the University of Groningen, however the nature of this position will require a lot of travelling for synchrotron and XFEL measurements. For this position we are looking for a recent PhD graduate with hands-on experience in membrane protein crystallography and experience in synchrotron and /or XFEL data collection and data processing. Position #2 - a 3 year PostDoc position in single particle cryo-EM on membrane proteins, based primarily at the Moscow Institute of Physics and Technology but with visits to the lab in Groningen as well. For this position we are looking for a recent PhD graduate with hands-on experience in membrane protein production (bacterial expression hosts or LEXSY) / purification and desirably some experience in single particle cryo-EM. The working language of the Institute is English, but knowledge of Russian can be helpful in everyday life. The Russian courses can be arranged if necessary. If you are interested, please send your CV and a motivation letter to a.guskov at rug.nl (for position #1) and to guskov.ai at phystech.edu (for position #2) Albert Guskov (Dr rer nat) Head of Biomolecular X-ray Crystallography lab | University of Groningen Head of Cryo-EM lab | Moscow Institute of Physics and Technology To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Postdoc position in structural biology
We have an opening for a PostDoc position in the field of structural biology at the Research Center for Molecular Mechanisms of ageing and age-related diseases at Moscow Institute of Physics and Technology ( https://mipt.ru/english/) to work on structural elucidation of membrane proteins by combination of X-ray crystallography and single particle cryo-EM. The suitable candidates should have a PhD in chemistry, biochemistry or biophysics with hands-on experience in either macromolecular crystallography or single particle cryo-EM, as well as experience in recombinant protein production and purification (experience with baculovirus expression system is a plus). The candidates should be fluent in English (knowledge of Russian is not required). We offer: A 2-year initial contract with the possibility of extension; Salary of ~ 2000 euro; The full support with all paperwork (visa and work permit); Young and ambitious team; Possibility of research visits to foreign partners laboratories; The subsidized housing on the campus; The rich cultural heritage and all kinds of attractions of Moscow city. Please send your application (a motivation letter, CV, names of two potential referees) to a.guskov at rug.nl and rogachev.av at phystech.edu no later than 31st of October To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] 2y PostDoc position @ University of Groningen
Dear all, I have an immediate opening for the 2y industry sponsored PostDoc position in Structural Biology. The project is about membrane-embedded / membrane-associated enzymes. The essential skills: membrane protein expression (bacterial and or yeast) and purification (IMAC + SEC), excellent level of English (both oral and written); Desirable skills: crystallisation / structure determination or experience in single-particle Cryo-EM. Salary according to the collective labour agreement (cao) of Dutch Universities: level 10.4. Applicants from outside The Netherlands might be eligible for 30% tax deduction. Please send your CV+motivation letter+1-2 recommendations (including one from your PhD supervisor) by 30th of April, 23:59 CET to the following e-mail: a.guskov at rug.nl with the header 'application for a PostDoc position' Please note, only shortlisted candidates will be notified. With kind regards, Albert Guskov (Dr) |Assistant Professor | Biomolecular X-ray Crystallography |University of Groningen Nijenborgh 7, Groningen 9747 AG, The Netherlands Tel: +31 50 363-4391 |Secretary: +31 50 363-4378 |E-mail: a.gus...@rug.nl| To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] PhD position in structural biology - membrane proteins
Dear all, I have an immediate opening for a PhD candidate in my lab. The starting date should be before 1st of January 2019. The position is fully funded for 4 years. For our recent work please check: Garaeva et al,, Nature Structural & Molecular Biology, 2018, doi: 10.1038/s41594-018-0076-y Santos et al., eLife, 2018, doi: 10.7554/eLife.35828 Gati& Stetsenko et al., Nature Communications, 2017, doi: 10.1038/s41467-017-01483-7 The application (including cv, a letter of motivation and names of two referees) should be submitted before 15th of August. See the attached file for more information. Albert To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 <> <>
[ccp4bb] Two PhD positions in membrane protein structural biology
Dear all, I have two openings in my lab to work on: (1) *TIME-RESOLVED CRYSTALLOGRAPHY*. This is a collaborative effort of several labs, including experts in structural biology (Guskov’s lab), biophysics and biochemistry (Slotboom’s lab), photopharmacology (Szymanski’s lab) and pharmaceutical biotechnology (Poelarends’ lab). The position is embedded into Guskov’s lab with the co-supervision from all other PIs. The general aim of the project is to study dynamic behaviour of amino acid transporters using novel photocontrolled effectors of amino acid transport within the context of our photopharmacology program. The specific aim for this PhD project is (i) to perform thorough biochemical / biophysical characterization of transport using in-house developed assays, and (ii) to assist with the structural studies (crystallization, data collection and refinement). and 2) *METAL TRANSPORT**.* The general aim of this project is to perform structural characterization of several medically relevant transporters involved in the transport of metals. This will include biochemical / biophysical characterization and structural (crystallography and Cryo-EM) investigations. Since these are the scholarship positions, the whole application process has to be done via the University's website. Please apply via https://www.rug.nl/education/phd-programmes/phd-scholarship-programme/phd-scholarships?details=00347-02S00066GP (position 1) or https://www.rug.nl/education/phd-programmes/phd-scholarship-programme/phd-scholarships?details=00347-02S00066FP (position 2) The deadline for applications is the 1st of April, with the envisaged starting date of the 1st of June With kind regards, Dr Albert Guskov, Assistant Professor / NWO-Vidi fellow, Biomolecular X-Ray Crystallography, University of Groningen, the Netherlands
[ccp4bb] Recent advances in Protein Crystallography - deadline for submission 15th December 2016!
Dear colleagues, this is a kind reminder that the deadline for the submission to the special issue 'Recent advances in Protein Crystallography' in the journal "Crystals' (MDPI, Switzerland) is in one month! weblink: http://www.mdpi.com/journal/crystals/special_issues/protein_crystallography We welcome your submissions (any form: review, short communications, original research, technical note) covering not only topics mentioned at the weblink above, but also protein crystallography and crystal structures in a broad sense. The deadline for submission is 15th of December 2016. The benefits of publishing in Crystals: Open Access Unlimited and free access for readers No Copyright Constraints Retain copyright of your work and free use of your article Thorough Peer-Review Coverage by Leading Indexing Services No Space Constraints, No Extra Space or Color Charges Discounts on Article Processing Charges (APC) If you belong to an institute that participates with the MDPI membership program (The default publishing fee is 800 CHF). Additionally many research institutes have special programs to promote publishing in open access manner. In case of any questions, feel free to contact me (Albert) directly With kind regards, Dr Albert Guskov (Guest editor) and Prof Dr Helmut Cölfen (Editor-in-chief)
[ccp4bb] Reminder: Towards novel therapies: Emerging insights from structural and molecular biology, 6-8 March 2017
Dear all, this is just to remind you that the deadline for the registration is fast approaching! (1st of December) In brief: we are organising a conference "Towards novel therapies: Emerging insights from structural and molecular biology" in the beautiful city of Groningen (the Netherlands) on 6-8 of March 2017. please see all the relevant information (list of speakers, location, registration link) at the following website: http://events.embo.org/17-structural-biol/ The deadline for registration is 1st of December, selected participants will be notified by 7th of December. In addition to the pleiad of eminent speakers we have reserved 10 spots for oral presentations, which will be selected from the submitted abstracts! We keep the registration fee as low as possible (100 euro for academia and 250 euro for industry), however participants have to arrange transport and accommodation themselves. For any further information please contact Ms Renate van der Tuuk Phone: +31 50 363 4139 Email: embo.gronin...@gmail.com or me (Albert) directly, with kind regards, Dr Albert Guskov, Prof Dr Dirk J Slotboom and Prof Dr Wim Hol
[ccp4bb] Gordon Research Conference On Ligand Recognition Molecular Gating (23-28 March)
Dear all, may I draw your attention to the following conference announcement: Join us at the 2014 Gordon Conference On Ligand Recognition Molecular Gating: Structure and Dynamics of Ion Channels, G-protein Coupled Receptors, and Solute Transporters (Ventura, CA March 23-28) The Gordon Research Conference on Ligand Recognition and Molecular Gating aims to share the latest knowledge on the functional mechanisms of ion channels, G-protein coupled receptors, and solute transporters. Specifically, the goal of the conference is to increase our understanding of how integral membrane proteins bind or recognize ligands (ions, small molecules, proteins), and how binding elicits conformational changes that lead to transport of the ligands across the membrane, the gating of channels, or the transmission of signals. There will be an emphasis on combining high-resolution structural data with information on dynamics to understand mechanisms. Keynote Speakers: Brian Kobilka, John Walker and Eric Gouaux For the complete program see: https://www.grc.org/programs.aspx?year=2014program=ligand The application form can be found at https://www.grc.org/application.aspx?id=12688 Note: Your approval for attendance is a 2-step process: (1) You apply and (2) Once you receive your notification of acceptance from GRC, then you can register. We look forward to seeing you in late March on the coast of California! Albert Guskov, on behalf of the Chair Dirk Jan Slotboom and V. Chair Crina Nimigean Albert GUSKOV (Dr) | Research Fellow | Membrane Enzymology | University of Groningen Nijenborgh 4, Groningen 9747 AG, The Netherlands Tel: (31) 50-363-3941 | Email: a.gus...@rug.nl |
[ccp4bb] Gordon Research Conference On Ligand Recognition Molecular Gating (23-28 March)
Dear all, may I draw your attention to the following conference announcement: Join us at the 2014 Gordon Conference On Ligand Recognition Molecular Gating: Structure and Dynamics of Ion Channels, G-protein Coupled Receptors, and Solute Transporters (Ventura, CA March 23-28) The Gordon Research Conference on Ligand Recognition and Molecular Gating aims to share the latest knowledge on the functional mechanisms of ion channels, G-protein coupled receptors, and solute transporters. Specifically, the goal of the conference is to increase our understanding of how integral membrane proteins bind or recognize ligands (ions, small molecules, proteins), and how binding elicits conformational changes that lead to transport of the ligands across the membrane, the gating of channels, or the transmission of signals. There will be an emphasis on combining high-resolution structural data with information on dynamics to understand mechanisms. Keynote Speakers: Brian Kobilka, John Walker and Eric Gouaux For the complete program see: https://www.grc.org/programs.aspx?year=2014program=ligand The application form can be found at https://www.grc.org/application.aspx?id=12688 Note: Your approval for attendance is a 2-step process: (1) You apply and (2) Once you receive your notification of acceptance from GRC, then you can register. We look forward to seeing you in late March on the coast of California! Albert Guskov, on behalf of the Chair Dirk Jan Slotboom and V. Chair Crina Nimigean Albert GUSKOV (Dr) | Research Fellow | Membrane Enzymology | University of Groningen Nijenborgh 4, Groningen 9747 AG, The Netherlands Tel: (31) 50-363-3941 | Email: a.gus...@rug.nl |
Re: [ccp4bb] Unknown density
Dear Pavel, you should also always consider your cryoprotectant molecules, so let's say if you used PEG for cryoprotection, there's a very high probability you may see it in your structure. It's very hard to say from the snapshots, but for the patch of density depicted in fig.2 I would try PEG (of course only if you had it). All the best, Albert 2013/2/25 Antony Oliver antony.oli...@sussex.ac.uk Dear Pavel, Is this density located on a symmetry axis? There is quite often a lot of noise around these regions - and it may not, in fact, be possible to model this satisfactorily. Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On Feb 25, 2013, at 10:03 AM, Natashin Pavel wrote: Hello everyone, I’m working on a structure with a 1.72Å resolution data and almost finished it. But there is a piece of unknown density between two protein molecules. The following pictures show this density from two sides: http://www.4sync.com/photo/WHewU7Ek/Density_1.html http://www.4sync.com/photo/RM3IEesw/Density_-_2.html This density is located between two protein molecules and is not connected to either of them. I have tried to fit several small organic molecules from crystallization conditions and protein sample buffer, also tried ligand database search using “Phenix ligand identification” software, but no satisfactory results. Crystallization condition: DL-Malic acid Sample Buffer: Bis-Tris, EDTA Reagents from protein purification step (also checked): Tris, Urea, Triton-X100, DTT. I will very much appreciate to hear any suggestions and ideas on what to do. Best regerds, Pavel V. Natashin PhD student Photobiology Laboratory Institute of Biophysics Russian Academy of Sciences Siberian Branch Krasnoyarsk 660036, Russia National Laboratory of Biomacromolecules Institute of Biophysics Chinese Academy of Sciences Beijing 100101, China
Re: [ccp4bb] Mac OS 10.8 Mountain Lion and CCP4?
Hi Brad, everything is working fine, both on laptop (Macbook pro) and PowerMac. Best regards, Albert 2013/2/21 Brad Bennett bradbennet...@gmail.com Hi all- Sorry if this has been gone over before but I could not find a direct answer after a cursory search in the archives and online. Is the CCP4 suite compatible with Mountain Lion? Specifically, the GUI (ccp4i) and Coot? Our Macs are running Leopard and Snow Leopard and we've been thinking of upgrading for awhile. Thanks! Brad
[ccp4bb] PEG refinement
Dear all, is there any consensus about PEG refinement? I'm currently refining several structures with a lot of bound PEG molecules. However I'm completely confused now which ligand description to use. For example, a search in Hic up database reveals 12 possible descriptions for PEG, 5 of them used for PEG400, but with completely different length ranging from C8 (number of carbon atoms), ligand ID PG4 up to C24, ligand ID 12P. Other descriptions are also quite confusable, for example PEG 8K (ligand id PEU) is C55H112O28, but apparently shorter PEG1500 (ligand id 15P) is C69H140O35. Shall the crystallography community come up with some standardised list of descriptions for PEG molecules? With best regards, Albert
Re: [ccp4bb] Xenon Derivatization
Hi Brennan, we did some time ago a kind of similar experiment, where we used Xe and Kr to contour the channels within Photosystem II (see Gabdulkhakov et al, Structure. 2009 Sep 9;17(9):1223-34 for the pressure, wavelength and derivatization time values we used) However before doing this we went the same way you're going now - we tried this technique with lysozyme crystals and as I remember it worked fantastically well and we could solve the structure by SAD within few minutes at the beam line. From your description it seems you're on the right scale of time and pressure and according to your table you have detectable anomalous signal. Are you sure you've calculated your anomalous map correctly? Have you solved the structure with SAD or first with MR? Best regards, Albert Albert GUSKOV (Dr) | Research Fellow | Division of Structural Computational Biology | Nanyang Technological University Proteos 7-01, Biopolis Drive 61, Singapore 138673 Tel: (65) 6586-9690 GMT+8h 2011/11/5 Brennan Bonnet brennan.bon...@lightsource.ca Hi everyone, My name is Brennan Bonnet and I am doing my Master’s project on SAD phasing of proteins using xenon gas. I plan on doing several proteins but first I am trying to get everything working smoothly on lysozyme since it is easy to grow, diffracts well, and is already known to bind xenon atoms (PDB entry 1C10, 3 sites @ 8bar pressure). Put simply, my method involves growing the crystals, mounting them in cryoloops, cryoprotection (if required), pressurization by xenon gas using the Hampton Xenon Chamber and quickly freezing them using liquid nitrogen with only a couple of seconds between depressurization and freezing. I have chosen pressures and durations of pressurization based on previous work which indicates that suitable derivatives may be produced using pressures between 1-100 bar and that binding should be complete within minutes. (see Use of Noble Gases Xenon and Krypton as Heavy Atoms in Protein Structure Determination by M. Schiltz, R. Fourme, and Thierry Prangé for a summary). Therefore I have chosen to use pressures between 7-28bar (100-400psi) for a duration of 15 minutes. After processing using XDS and solving with Phenix, the results show occupancies 0.1 which indicate no xenon binding or at least nothing that “sticks out”. The general trend is that increased xenon pressure results in a stronger anomalous signal and I have attached a table below with some processed data from XDS. I plan on trying a couple of other things. I have been collecting at 7keV but plan to try 6keV in order to get closer to the xenon L-edges and get a better anomalous signal. I also plan on trying longer pressurization times up to an hour to hopefully get better occupancy. Has anyone had any success with this method or any sort of “Aha!” moment? Help in the matter would be much appreciated. Set Pressure Energy Anom MaxAnom Total Anom Max / Anom Total Rmeas Resolution Last shell I/σ(I) (psi)(keV) (%) (Å) Sep7100 7 2.111 1.352 1.56139053342.03 13.9 Sep7160 7 1.935 1.244 1.5554662384.7 2.03 12.17 Sep7200 7 2.454 1.293 1.8979118333.4 2.03 11.01 Jul28 200 7 3.13 1.7491.7895940542.2 2.03 17.6 Sep7280 7 2.375 1.54 1.5422077923.1 2.03 14.33 Jul28 400 7 3.082 1.649 1.8690115223.5 2.03 14.29 Thanks, ~Brennan~
Re: [ccp4bb] Symmetry Related molecules
Hi Yuri, have a look at SuperSym plugin for pymol http://www.pymolwiki.org/index.php/SuperSym Best regards, Albert *Albert GUSKOV (Dr) *| Research Fellow | Division of Structural Computational Biology | Nanyang Technological University Proteos 7-01, Biopolis Drive 61, Singapore 138673 Tel: (65) 6586-9690 GMT+8h | Cell: (65) 8366-2779 | Email: a.gus...@ntu.edu.sg | Web: www.ntu.edu.sg 2011/8/5 Yuri yuri.pom...@ufl.edu Whats the best way to visualize all the symmetry related molecules, I know COOT will show them as backbone. I was looking for publication quality images...PyMol maybe? thank you for suggestions -- Yuri Pompeu
Re: [ccp4bb] Bypassing phase separation for nice crystals.
Hi Timur, have you tried seeding from your microstalline stuff? Might be worth to try! Cheers, Albert Albert GUSKOV (Dr) | Research Fellow | Division of Structural Computational Biology | Nanyang Technological University Proteos 7-01, Biopolis Drive 61, Singapore 138673 Tel: (65) 6586-9690 GMT+8h | Cell: (65) 8366-2779 | Email: a.gus...@ntu.edu.sg | Web: www.ntu.edu.sg 2011/7/18 F. Timur Senguen ftseng...@gmail.com Hi everyone, I have been issues with a particular protein. I have been close for a while, but yet so far. Rather than going from a clear drop to crystal, my protein first undergoes phase separation (large oily drops) in which one phase contains most, if not all, of the protein. This phase separation occurs within a day of preparing the drop. A day after phase separation the oily phase is now a large disordered crystalline mass which does not diffract very well. I have tried changing buffer concentrations, precipitant amounts, ionic strengths and pH and in all cases this phenomenon is observed. I even screened protein concentrations to see if reducing protein concentration would prevent the phase separation. Is there any way to bypass this phase separation, which I think prevents me from obtaining nice crystals. Should I try detergents, chaotropes, or other additives? Thanks in advance. Timur -- F. Timur Senguen, Ph.D. Postdoctoral Research Fellow Boston Biomedical Research Institute 64 Grove Street, Watertown, MA 02472 USA
Re: [ccp4bb] MOSFILM
According to Harry Powell's website: The current version of Mosflm is version 7.0.7 (uploaded onto this site 22nd December 2010). link: http://www.mrc-lmb.cam.ac.uk/harry/mosflm Cheers, Albert 2011/3/13 REX PALMER rex.pal...@btinternet.com Is MOSFILM 6.2.6 the latest version? Rex Palmer Birkbeck College
Re: [ccp4bb] .pir file
Hi Careina, just change extension of your sequence file, i.e.: change yoursequencefile.extension (where extension could be .txt .fasta, etc) to yoursequencefile.pir It should work then. Cheers, Albert Albert GUSKOV (Dr) | Research Fellow | Division of Structural Computational Biology | Nanyang Technological University Proteos 7-01, Biopolis Drive 61, Singapore 138673 Tel: (65) 6586-9690 GMT+8h | Cell: (65) 8366-2779 | Email: a.gus...@ntu.edu.sg | Web: www.ntu.edu.sg 2011/2/18 Careina Edgooms careinaedgo...@yahoo.com: Dear CCP4 mailing list I have a relatively simple question. How do I get sequence file in .pir format which is required for many programs? I normally use fasta format but some programs eg arpwarp do not allow me to use that Thanks for your help Careina
Re: [ccp4bb] Saxs reviews or books
Hi, you can check this page http://www.embl-hamburg.de/biosaxs/embo10.html there are several presentations plus recommended reading list. Cheers, Albert Albert GUSKOV (Dr) | Research Fellow | Division of Structural Computational Biology | Nanyang Technological University Proteos 7-01, Biopolis Drive 61, Singapore 138673 Tel: (65) 6586-9690 GMT+8h | Cell: (65) 8366-2779 | Email: a.gus...@ntu.edu.sg | Web: www.ntu.edu.sg 2011/1/11 Rojan Shrestha ro...@riken.jp: Hello: I am very novice about Small Angle X-ray Scattering. I am looking for introductory books or review papers. Could you recommend this type of document? Regards, Rojan
Re: [ccp4bb] Coot density fit analysis with mtz from PHENIX 1.6.4
Dear all, I noticed the same problem on Mac OSX (snow leopard) . Seems to be an issue for all phenix installation packages for current release. Cheers, Albert Guskov, Dr rer nat Medical Structural Biology, Nanyang Technological University, Singapore On Sunday, November 28, 2010, Tanner, John J. tanne...@missouri.edu wrote: Dear CCP4BB, Has anyone encountered the following problem when using Coot (coot-0.6.2pre) validate density fit analysis with an mtz file calculated using phenix.refine (1.6.4)? All of the density fit values are exactly 0.0 (all bars same height and red) when using a 2Fo-Fc map calculated from an mtz file output by PHENIX Version: 1.6.4, Release tag: 486, Platform: intel-linux-2.6 redhat-e5.5. Density fit analysis worked fine when I was using mtz files from PHENIX Version: 1.6.2, Release tag: 432, Platform: intel-linux-2.6 redhat-e5.5. Thus, it appears to be an issue with the new version of phenix. I should mention that the maps from 1.6.4 mtz files display fine in Coot and real space refinement against those maps in Coot works fine too. It is just the density fit analysis utility that seems to be problematic. Thanks, Jack Tanner -- John J. Tanner Professor of Chemistry and Biochemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-2754 Email: tanne...@missouri.edu http://www.chem.missouri.edu/TannerGroup/tanner.html
Re: [ccp4bb] software for predicting protein solubility, stabililty and disorders
Hi Vikrant, I guess Xtalpred server might be of interest for you. check it at http://ffas.burnham.org/XtalPred-cgi/xtal.pl Cheers, *Albert GUSKOV (Dr) *| Research Fellow | Division of Structural Computational Biology | Nanyang Technological University Proteos 7-01, Biopolis Drive 61, Singapore 138673 Tel: (65) 6586-9690 GMT+8h | Cell: (65) 8366-2779 | Email: a.gus...@ntu.edu.sg | Web: www.ntu.edu.sg 2010/7/29 vikrant saa powervikr...@yahoo.co.in I want to do cloning of a 40 Kd protein in pRSETA, and pGEX-KT vector. I don't have any idea about protein solubility, its multimeric form, stability and disorder etc. There is nothing known in the literature also. Is there any software that can predict these parameters, so that i can decide which domain i need to clone for soluble and stable protein purification. *Vikrant *** ***Junior Research Fellow (CSIR) * *Lab No. 101, Dr. Varma Lab* *Cancer Research Institute Advance Centre for Treatment, Research and Eduction in Cancer (ACTREC) Tata Memorial Hospital, Kharghar, Navi Mumbai-410210 * #
[ccp4bb] Coot save file error under Mac OSX
Dear all, I've installed coot with fink, everything works fine, except the fact I can not solve results of my work (that makes it totally senseless ;-)) The error I get is Gtk-WARNING **: Unable to find default local directory monitor type Could someone point me out what is wrong? Kind regards, Albert Guskov, Freie Universitaet Berlin Fachbereich Biologie, Chemie, Pharmazie Institut fur Chemie/Kristallographie
[ccp4bb] problem with ccp4-6.1.0 installation on Mac OS X
Dear all, after sourcing ccp4.setup-sh file and trying to launch ccp4i, I
continuously get the following error message: Top level CCP4 directory is
/usr/local/ccp4-6.1.0
Using CCP4 programs from /usr/local/ccp4-6.1.0/bin
Error in startup script: wrong # args: should be dbccp4i_open_project
project args
while executing
dbccp4i_open_project
(eval body line 1)
invoked from within
eval dbccp4i_open_project $project $args
(procedure DbLoadFile line 12)
invoked from within
DbLoadFile $project
(procedure DbOpenDatabase line 13)
invoked from within
DbOpenDatabase $project
(procedure DbOpen line 30)
invoked from within
DbOpen -init
(procedure DbInitialise line 19)
invoked from within
DbInitialise
(procedure taskbrowser line 38)
invoked from within
$system(RUN_MODE)
(default arm line 9)
invoked from within
switch $system(RUN_MODE) \
script {
# Run a script ($CCP4I/scripts/project.script) with parameters from def file
source [file join $env(CCP4I_...
(file /usr/local/ccp4-6.1.0/share/ccp4i/bin/ccp4i.tcl line 163)
invoked from within
source [file join $env(CCP4I_TOP) bin ccp4i.tcl]
(file /usr/local/ccp4-6.1.0/bin/ccp4i line 5)
__
Can anyone point me to what I'm doing wrong? CCP4 is installed by default to
/usr/local/ccp4-6.1.0 I've also installed TclTk v8.4.18 from CCP4 download
pages and changed ccp4.setup-sh file (I'm using bash) accordingly.
With best wishes,
Albert Guskov,
Freie Universitaet Berlin
Fachbereich Biologie, Chemie, Pharmazie
Institut fur Chemie/Kristallographie
[ccp4bb] ccp4-6-1-0 installation on Mac OS X
Dear all, after sourcing ccp4.setup-sh file and trying to launch ccp4i, I
continuously get the following error message: Top level CCP4 directory is
/usr/local/ccp4-6.1.0
Using CCP4 programs from /usr/local/ccp4-6.1.0/bin
Error in startup script: wrong # args: should be dbccp4i_open_project
project args
while executing
dbccp4i_open_project
(eval body line 1)
invoked from within
eval dbccp4i_open_project $project $args
(procedure DbLoadFile line 12)
invoked from within
DbLoadFile $project
(procedure DbOpenDatabase line 13)
invoked from within
DbOpenDatabase $project
(procedure DbOpen line 30)
invoked from within
DbOpen -init
(procedure DbInitialise line 19)
invoked from within
DbInitialise
(procedure taskbrowser line 38)
invoked from within
$system(RUN_MODE)
(default arm line 9)
invoked from within
switch $system(RUN_MODE) \
script {
# Run a script ($CCP4I/scripts/project.script) with parameters from def file
source [file join $env(CCP4I_...
(file /usr/local/ccp4-6.1.0/share/ccp4i/bin/ccp4i.tcl line 163)
invoked from within
source [file join $env(CCP4I_TOP) bin ccp4i.tcl]
(file /usr/local/ccp4-6.1.0/bin/ccp4i line 5)
__
Can anyone point me to what I'm doing wrong? CCP4 is installed by default to
/usr/local/ccp4-6.1.0 I've also installed TclTk v8.4.18 from CCP4 download
pages and changed ccp4.setup-sh file (I'm using bash) accordingly.
With best wishes,
Albert Guskov,
Freie Universitaet Berlin
Fachbereich Biologie, Chemie, Pharmazie
Institut fur Chemie/Kristallographie
[ccp4bb] Anion binding sites in proteins
Dear all, can someone point me to something similar to Metal coordination sites in proteins (http://tanna.bch.ed.ac.uk), but describing anions (I'm mainly interested in chloride-binding sites)? Thank You, Albert -- Albert Guskov, Freie Universitaet Berlin Fachbereich Biologie, Chemie, Pharmazie Institut fur Chemie/Kristallographie
