[ccp4bb] Coot 0.6: new binaries and NEW CITATION
Two things for Coot users... Firstly, I have just uplaoded the remaining Linux binaries for Coot 0.6, i.e. Fedora 8, Fedora 10 and Ubuntu 6.06 (with python and gtk2 gui). You can find them on the Coot website here: http://www.biop.ox.ac.uk/coot/software/binaries/releases/ Secondly, please could you stop citing the 2006 Coot paper from today! Specifically, do not cite Emsley and Cowtan (2006) Acta Cryst D62 because by doing so you rob Bernhard Lohkamp and Bill Scott of the well deserved credit for their work. Instead, could you cite the following paper: Emsley P, Lohkamp B, Scott W, Cowtan K (2010) Features and Development of Coot Acta Cryst D66 (in press) Thanks! Kevin
Re: [ccp4bb] Error in CAD during ARP/wWARP run in sharp/autoSHARP - also posted in sharp discuss
Well - cad cant work with that script so somehow it is being generated wrongly, presumanly in Arp/warp stage.. It would need input such as: LABIN FILE 1 E1=FBshasol E2 = something - presumably SIGFBshasol Eleanor Narayanan Ramasubbu wrote: Hi: Sorry for the same posting in here as well but I thought may be some of you might have encountered the same problem but may not be subscribing to sharp list. I am trying run sharp/autoSHARP on a mac (os x 10.4) using the guven example file: krel1-SAD.0 I am getting an error at the CAD as provided below ++ The parameter file is: /Users/subbu/sharp/sharpfiles/logfiles_local/krel-SAD.1/wARP_49.4pc/20091213_080749/arp_warp_tracing.par Entering warp_tracing.sh from the command line The working directory is: /Users/subbu/sharp/sharpfiles/logfiles_local/krel-SAD.1/wARP_49.4pc/20091213_080749 ARP/wARP will run in the subdirectory: temp_tracing Building free atoms model Initial map will be calculated with pre-weighted amplitudes ... CAD: Error in label assignments in LKYSET QUITTING ... ARP/wARP module stopped with an error message: CAD ++ The relevant CAD log file is also attached below Chosen Asymmetric unit of reciprocal space: [mmm] hkl:h=0, k=0, l=0 ** Missing flag set in HKLIN1 to Nan: ** Missing entries LISTED as -999.000 Data line--- LABIN E1=FBshasol E2 MtzParseLabin: run out of labels trying to match E2 CAD: Error in label assignments in LKYSET ++ This happened on another dataset so I wanted to see whether the example file runs ok. Please help Subbu
Re: [ccp4bb] MR question
The 2nd peak is a shoulder of the origin peak at 1.0 0 0 so should be ignored.. The 3rd peak is 16% of the origin - rather marginal I would say. So I dont think there is clear evidence of translational NCS Eleanor Sylvia Fanucchi wrote: Morning all Apologies for the simple question. I have a structure I would like to solve using molecular replacement. I am a bit confused by the patterson peaks. There appears to be a large non-origin peak (although it is apparently symmetry-related to the origin?). Does this mean that there is some translation occurring in the asymmetric unit? Or is there non-crystallographic symmetry? Does anyone know what I should do to address this? I have continued with the molecular replacement as normal and did not get a solution with Phaser. Molrep gives a solution that appears correct based on the maps and refines reasonably well. Count Site HeightGrid Fractional coordinates Orthogonal coordinates 11100.00 0 0 0 0. 0. 0. 0.00 0.00 0.00 21 67.1633 0 0 0.9706 0. 0.41.11 0.00 0.00 32 16.5910 0 2 0.3070 0. 0.030413.00 0.00 2.51 43 16.5424 0 2 0.6920 0. 0.031729.30 0.00 2.63 54 14.2417 0 3 0.5034 0. 0.044721.31 0.00 3.70 65 14.1920 0 3 0.5763 0. 0.050724.40 0.00 4.20 Best regards Sylvia Fanucchi Ph.D Protein Structure-Function Research Unit East Campus, Gate House Room 416 School of Molecular and Cell Biology University of the Witwatersrand Johannesburg 2050 South Africa Tel: +27 (11) 717-6348 Fax: +27 (11) 717-6351 E-mail: sylvia.fanuc...@wits.ac.za mailto:sylvia.fanuc...@wits.ac.za htmlpfont face = verdana size = 0.8 color = navyThis communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary./font/p/html
[ccp4bb] question about refmac/coot findwater
Hi, This question may have been asked before, so please excuse me for re-posting it. I notice that when I do a round of 10 cycles of refmac combined with (5cycles, 3 sigma level, 1.4 A resolution) of findwaters in coot, some water molecules from the different coot cycles fall one on top of the other. Does that mean that coot does not check for clashes between water molecules detected in previous cycles ? And in any case, does coot put another water molecule in the same place (or nearly) because there is still residual difference density after placing the first one ? I assume that this happens here, which in fact can be beneficial in my current structure where I'm also trying to locate chloride ions (I don't have anomalous data in the correct wavelength so I can't depend on that). Please advise. Thanks. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan
[ccp4bb] Postdoctoral position in NYC
A funded postdoctoral position is availableimmediately in Weill Cornell Medical College in New York City. The research focus will be on thecrystallography-based study of the structure and function of membrane transporters.The laboratory is fully equipped and has regular access to crystallizationrobot, in-house X-ray diffractometer and synchrotron beamlines. A successful candidate will have arecent PhD degree in biochemistry, biophysics, structural biology or a relatedfield and will be an expert in at least some quantitativemethods/approaches. Crystallographic experience is not essential, but an establishedinterest in membrane proteins is. Please e-mail your CV, cover letter and names/contact info of tworeferences to Olga Boudker: olb2...@med.cornell.edu. -- Olga Boudker Assistant Professor Department of Physiology and Biophysics Weill Cornell Medical College olb2...@med.cornell.edu Tel. (212) 746-6634
[ccp4bb] 2010 Hybrid Methods Symposium Abstract Deadline Today
Dear Colleagues: This is a reminder that today is the deadline for Early Registration and Abstract Submission for the 2010 Symposium on Structural Analysis of Supramolecular Assemblies by Hybrid Methods. The Symposium will be held at Granlibakken Conference Center, Lake Tahoe, California, and the dates are March 10-14, 2010. The overall goal of the Symposium is to illustrate the power of combining state of the art methods to tackle important and challenging biological problems and to identify limitations and gaps in currently practiced hybrid methods. We are fortunate to have recruited two outstanding Keynote Speakers: Stephen C. Harrison (Harvard) and Thomas D. Pollard (Yale), as well as a great program of platform speakers who utilize multiple approaches to investigate the structural biology of complex biological systems. Further details and registration information can be obtained at our website: http://www.hybridmethods2010.com/index.html. Note that a series of platform and workshop talks will also be selected from submitted abstracts, which will enable us to feature hot emerging topics and to provide qualified students and postdocs with the opportunity to present their work. The Symposium builds on a series of very successful previous meetings on the same theme from 2004-2008. The central premise is that gaining a comprehensive understanding of the highly sophisticated machines, complexes, and organelles of the cell requires the coordinated application of a number of complementary biophysical approaches (hybrid methods). A new innovation at the 2010 meeting will be a special workshop on Harnessing Different Wavelengths of Electromagnetic Radiation, which will feature the rapidly developing fields of subdiffraction light microscopy and other emerging imaging techniques (e.g., X-ray tomography), as well as new advances within more traditional hybrid approaches such as the interfaces between electron microscopy, X-ray crystallography, and computational biology. Featured topics will also include other biophysical methods, proteomics and cell biology. The meeting will be divided into seven Scientific Sessions and one Special Methods Workshop Session I: Hybrid Approaches to Macromolecular Filaments Session II: Hybrid Approaches to Membrane Complexes Session III: Hybrid Approaches to Dynamic Assemblies Session IV: Computational Approaches to Hybrid Analyses Session V: Hybrid Approaches to Global Analyses Session VI: Hybrid Approaches to Cell Biology Session VII: Hybrid Approaches to Nanomachines Special Methods Workshop: Harnessing Different Wavelengths of Electromagnetic Radiation We hope to see you there for four days of exciting science (as well as some outstanding skiing!). Sincerely yours, The Organizing Committee: Wes Sundquist, Chair Phoebe Stewart, Co-Chair Dorit Hanein, Nobutaka Hirokawa, Felix Rey, Alasdair Steven, and Bill Weis. Rachel Bookman, Conference Secretariat.
[ccp4bb] When can I say the refinement is done?
Hi, All, I have a general question for refinement. I tried to refine a dataset that is about 2.3A and got R/Rfree is about o.18/0.24. RMS(angles): 0.77, RMS(bonds): 0.003 however, when I check with molprobity, There are still some outliers and some bad contact that is overlap 0.4 A. Ramachandran outliers: 0.2% (Goal: 0.2%) Ramachandran favored: 97.7% (Goal: 98%) Rotamer outliers: 1.4% (Goal: 1%) C-beta outliers: 0(Goal: 0) Clashscore: 14.16 Generally speaking, should I remove all those bad contact or is there any miminum requirement that ok, the structure is acceptable? I know the refinement can be endless, but I just want to get an idea how far away I'm . Thanks. R
Re: [ccp4bb] When can I say the refinement is done?
Hi, the exact answer to your question is here: http://cci.lbl.gov/~afonine/for_ak/validation.pdf In particular, your question below is spelled out is discussed staring from slide #2. Pavel. On 12/14/09 7:50 AM, rui wrote: Hi, All, I have a general question for refinement. I tried to refine a dataset that is about 2.3A and got R/Rfree is about o.18/0.24. RMS(angles): 0.77, RMS(bonds): 0.003 however, when I check with molprobity, There are still some outliers and some bad contact that is overlap 0.4 A. Ramachandran outliers: 0.2% (Goal: 0.2%) Ramachandran favored: 97.7% (Goal: 98%) Rotamer outliers: 1.4% (Goal: 1%) C-beta outliers: 0(Goal: 0) Clashscore: 14.16 Generally speaking, should I remove all those bad contact or is there any miminum requirement that ok, the structure is acceptable? I know the refinement can be endless, but I just want to get an idea how far away I'm . Thanks. R
Re: [ccp4bb] When can I say the refinement is done?
A less exact answer, albeit less precise and informative than the very nice PDF and the very useful Polygon ideas, is: very well done, but have another look at this couple of Ramachandran outliers and also consider loosening up the geometry a bit. ;-) A. On Dec 14, 2009, at 17:04, Pavel Afonine wrote: Hi, the exact answer to your question is here: http://cci.lbl.gov/~afonine/for_ak/validation.pdf In particular, your question below is spelled out is discussed staring from slide #2. Pavel. On 12/14/09 7:50 AM, rui wrote: Hi, All, I have a general question for refinement. I tried to refine a dataset that is about 2.3A and got R/Rfree is about o.18/0.24. RMS(angles): 0.77, RMS(bonds): 0.003 however, when I check with molprobity, There are still some outliers and some bad contact that is overlap 0.4 A. Ramachandran outliers: 0.2% (Goal: 0.2%) Ramachandran favored: 97.7% (Goal: 98%) Rotamer outliers: 1.4% (Goal: 1%) C-beta outliers: 0(Goal: 0) Clashscore: 14.16 Generally speaking, should I remove all those bad contact or is there any miminum requirement that ok, the structure is acceptable? I know the refinement can be endless, but I just want to get an idea how far away I'm . Thanks. R P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
[ccp4bb] H32 or R 3 2 :H
hypFdemo_28.pdb: CRYST1 58.351 58.351 155.876 90.00 90.00 120.00 R 3 2 :H 1 I dont hold a candle for either of these SGs but Phaser is now outputting the R 3 2 :H and many many other CCP4 programs are then falling over Can the symlib be modified to accept both? Eleanor
[ccp4bb] CALL FOR ESRF SYNCHROTRON BEAM TIME WITH ONLINE MICOSPEC AT BEAMLINE ID14-2 (19th to 22nd of February 2010)
-- CALL FOR PROPOSALS FOR BEAMTIME WITH ONLINE MICROSPEC *Proposal Deadline 13th of January 2010* There will be beamtime available at the ESRF for MX data collection with a setup that allows online monitoring of UV/VIS spectral changes of the crystal during the X-ray diffraction experiment. Users who are interested in using this beam time (including those who are members of BAG Groups) should use the following mechanism: http://www.esrf.fr/UsersAndScience/UserGuide/Applying/ProposalGuidelines/MXnon-BAGproposal and it must be clearly indicated in the title of the proposal form that the online monitoring of spectral changes is necessary for the project. A brief description of the device is given below. However, Users are encouraged to consult the web pages for detailed information: http://www.esrf.fr/UsersAndScience/Experiments/MX/How_to_use_our_beamlines/Run_Your_Experiment/Microspectrophotometer_User_Guide As this is not a standard setup, it might take a significant amount of time to train users, align the device, and analyze the data in order to derive relevant data collection schemes. We will therefore schedule 24 hours for each project. The deadline for this specific application is 13th of January 2010. It is strongly recommended to record beforehand an absorption (fluorescence) spectrum of the crystal on a home microspectrophotometer such as the 4dx one, or at an off-line facility such as the ESRF Cryobench, and to provide it in the application form. Such a spectrum would greatly help to determine the feasibility of the experiment. For optimal experimental conditions, crystals should be frozen in minimal amounts of cryosolution, especially when the crystals are small. Finally, please note that the ESRF sample changer cannot be operated at the same time as the on-line microspec. *Dates of beam-time: 19th to 22nd of February 2010 *Storage Uniform Filling (200mA) Beamline: ID14-2 Energy: 13.29 keV Specifications: UV/VIS-range: 250 - 1100 nm ODmax: 2 - 2.5 Minimum integration time: 50 ms Light source: Mikropack DH-2000-BAL (Deuterium/Halogen) Monitoring light focal spot diameter: 0.03 (min) - 0.15 mm (max) Sampling freq (to disk): 10Hz or lower attachment: david_flot.vcf
Re: [ccp4bb] When can I say the refinement is done?
This is pointed out (in absolutely unobvious way - I wish I can add voice to that PDF) at the slide #19 -:) (except loosening weights). P. On 12/14/09 8:35 AM, Anastassis Perrakis wrote: A less exact answer, albeit less precise and informative than the very nice PDF and the very useful Polygon ideas, is: very well done, but have another look at this couple of Ramachandran outliers and also consider loosening up the geometry a bit. ;-) A. On Dec 14, 2009, at 17:04, Pavel Afonine wrote: Hi, the exact answer to your question is here: http://cci.lbl.gov/~afonine/for_ak/validation.pdf http://cci.lbl.gov/%7Eafonine/for_ak/validation.pdf In particular, your question below is spelled out is discussed staring from slide #2. Pavel. On 12/14/09 7:50 AM, rui wrote: Hi, All, I have a general question for refinement. I tried to refine a dataset that is about 2.3A and got R/Rfree is about o.18/0.24. RMS(angles): 0.77, RMS(bonds): 0.003 however, when I check with molprobity, There are still some outliers and some bad contact that is overlap 0.4 A. Ramachandran outliers: 0.2% (Goal: 0.2%) Ramachandran favored: 97.7% (Goal: 98%) Rotamer outliers: 1.4% (Goal: 1%) C-beta outliers: 0(Goal: 0) Clashscore: 14.16 Generally speaking, should I remove all those bad contact or is there any miminum requirement that ok, the structure is acceptable? I know the refinement can be endless, but I just want to get an idea how far away I'm . Thanks. R *P** **please don't print this e-mail unless you really need to* Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
[ccp4bb] announcement EMBO Practical Course : Scientific Programming and Data Visualisation for Structural Biology
Course Announcement EMBO Practical Course : Scientific Programming and Data Visualisation for Structural Biology We are pleased to announce our practical course Scientific Programming and Data Visualisation for Structural Biology offered at the newly constructed Advanced Training Center, EMBL, Heidelberg, Germany from May 5-7, 2010. The course is designed primarily for structural biologists (scientists from other disciplines are welcomed to apply). The goals of the course is to allow students to learn and master computational skills that are frequently required in less routine projects, and to learn methods of data visualization. Lecture sessions will cover data animation, Python programming for Molecular Dynamics and Drug Design, GUI development and high performance computing as well as modern programming tools on OSX. Three (3) parallel tutorial tracks will be offered (you can only select one): Molecular Visualization with Maya. Scientific Programming with Python, OS X Programming. As part of this course each participant will initiate a project relevant to their own research area, using the newly acquired skills. Attendees are also invited to present a poster (describing their research), that would benefit from molecular visualization or new software tools. There are several fellowships available! Deadline to submit your application is January 17, 2010, Register Today. Tutorial Lecturers: Alex Griekspor - Developer of the Papers Gaël McGill - Expert in Molecular Movies and Animation - to view examples of his work visit MolecularMovies.org. Ian Stokes-Rees - Harvard University Python programmer, with extensive experience in teaching. Joint lectures will be presented by expert programmers with extensive experience in structural biology and computational approaches: Kathryn Loving - Scientist from Schrodinger, will discuss utilizing Python in docking and macromolecular simulations. Bernhard Lohkamp - Karolinska Institute, will discuss designing graphical user interfaces with Python. For additional information please visit the course website. Comments from previous participants: Fantastic workshop. Getting software developers and experimental biologists to talk the same language is essential.; The OS X course was informative and very interesting. Until this class I did not know anything about all the excellent developer tools available for writing OS X programs, and I had no idea that OS X programming would be this approachable for novices. [...] the Python tutorial was understandably constrained in terms of its depth. However, I think maintaining a focus on the fundamentals [...] will provide a useful foundation for those who want to apply the skills on their own. Gaël McGill gave a brilliant [molecular animation] presentation and tutorial. Please feel free to e-mail Piotrek Sliz or Daniel Panne, if you have any questions. -- Daniel Panne, PhD EMBL Group leader Structure and Function of Macromolecular Assemblies pa...@embl.fr Tel: +33 476 207925 Fax: +33 476 207199 Web: http://www.embl.fr Postal address: EMBL, 6 Rue Jules Horowitz, BP181, 38042 Grenoble Cedex 9, France
Re: [ccp4bb] H32 or R 3 2 :H
Disclaimer: Phaser is the greatest MR program I've ever seen. However: The Hermann-Mauguin space group symbol is given without parenthesis, e.g., P 21 21 2 and using the full symbol, e.g., C 1 2 1 instead of C 2. -- The RCSB http://deposit.rcsb.org/adit/docs/pdb_atom_format.html I don't understand why specifications aren't consulted. It seems a lot easier to create a record that conforms to the most widely accepted specification than to invent a parser that can read any format one can possibly imagine. /Rant James On Dec 14, 2009, at 9:04 AM, Eleanor Dodson wrote: hypFdemo_28.pdb: CRYST1 58.351 58.351 155.876 90.00 90.00 120.00 R 3 2 :H 1 I dont hold a candle for either of these SGs but Phaser is now outputting the R 3 2 :H and many many other CCP4 programs are then falling over Can the symlib be modified to accept both? Eleanor
[ccp4bb] 3D search for peptide conformers?
I have a 10-residue stretch of a protein that adopts an interesting conformation; I'd like to know if this conformation occurs in other proteins. I'd welcome suggestions for tools that will allow me to to search for this peptide conformation in the PDB. I naturally thought of DALI, but it seems to require a minimum length of 30 residues. Thanks, Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
Re: [ccp4bb] H32 or R 3 2 :H
I believe that Coot also outputs R 3 2 :H (Paul can clarify). /start minor rant We need some standardization on the hexagonal setting for R32. Having just suffered through a fairly brutal structure determination in this space group, I can say that there are some 'issues' with this. For instance HKL outputs a line with the spacegroup set as R32 but the cell axes being for the hexagonal setting. If you import this into CCP4, it is not detected as H32, rather, it stays as R32 and problems ensue. So based on my recent experience, there are apparently three, not mutually acceptable, ways to denote the hexagonal setting of R32: R32 H32 R32 :H Can't we all just get along? /end minor rant -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Eleanor Dodson Sent: Monday, December 14, 2009 12:05 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] H32 or R 3 2 :H hypFdemo_28.pdb: CRYST1 58.351 58.351 155.876 90.00 90.00 120.00 R 3 2 :H 1 I dont hold a candle for either of these SGs but Phaser is now outputting the R 3 2 :H and many many other CCP4 programs are then falling over Can the symlib be modified to accept both? Eleanor Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
[ccp4bb] Postdoctoral position in structural studies of membrane proteins by electron crystallography (cryo-EM) and X-ray crystallography
Postdoctoral position in structural studies of membrane proteins by electron crystallography (cryo-EM) and X-ray crystallography A postdoctoral position is available in the School of Biology at the Georgia Institute of Technology (Georgia Tech). The laboratory has a main focus on structure-function studies of eukaryotic membrane proteins by two-dimensional crystallization and electron crystallography. The postdoctoral position will involve structure-function studies by electron crystallography and X-ray crystallography, and we are looking for a highly motivated individual with a background in structural biology and/or membrane protein biochemistry. Georgia Tech has an exceptionally interdisciplinary atmosphere, with open and frequent communication between departments. It is located in central Atlanta with among others the CDC and Emory University in the vicinity. Interested candidates should send the following information to the address below: a CV including a publication list, and the names and contact information for 3 references. -- Ingeborg Schmidt-Krey, Ph.D. Assistant Professor Georgia Institute of Technology School of Biology 310 Ferst Drive, Rm A118 Atlanta, GA 30332-0230 U.S.A. Phone 404-385-0286 Fax 404-894-0519 ingeborg.schmidt-k...@biology.gatech.edu http://www.biology.gatech.edu/faculty/ingeborg-schmidtkrey/
[ccp4bb] 3D search for peptide conformers? - SSM
Mon, Dec. 14th 2009 London Hello, I think you can you SSM Secondary Structure Matching at PDBe http://www.ebi.ac.uk/msd-srv/ssm/ you can upload your coordinate file and try to match to the whole of PDB. Hope it helps Miri On Mon, 14 Dec 2009, Patrick Loll wrote: I have a 10-residue stretch of a protein that adopts an interesting conformation; I'd like to know if this conformation occurs in other proteins. I'd welcome suggestions for tools that will allow me to to search for this peptide conformation in the PDB. I naturally thought of DALI, but it seems to require a minimum length of 30 residues. Thanks, Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu Dr Miri Hirshberg European Bioinformatics Institute UK PDBe - EBI -EMBL http://www.ebi.ac.uk/pdbe Phone: +44 (0) 1223 492647 FAX: +44 (0) 1223 494468
Re: [ccp4bb] H32 or R 3 2 :H
Hi Stephen, R32 H32 R32 :H Correct. These are all hexagonal setting. As far as I know, the hexagonal setting of R32 (R32:H) is the first one that comes up in the ITvA as is listed a R32. The rhombohedral/primitive setting of R32 (R32:R) comes second in the ITvA, I guess the first setting takes precedence. H32 is a pdb/ccp4ism. In my cctbx-skewed view, it looks like this: R32 == R32:H (== H32; not supported by the cctbx) R32:R is the primitive setting of R32:H Appending the setting to the space group makes life easier (no ambiguities) and you can do more funky stuff if one has the stomach/need to do so [like P212121 (a+b,a-b,c) ]. HTHP
Re: [ccp4bb] H32 or R 3 2 :H
Thanks Peter. The unfortunate thing is that not all of the programs are able to understand these different notations, and that they preferentially use different ones. It would be nice if we all agreed to standardize. I, personally, have no problem with R 3 2 :H since that is what it really is. Steve -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Peter Zwart Sent: Monday, December 14, 2009 4:08 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] H32 or R 3 2 :H Hi Stephen, R32 H32 R32 :H Correct. These are all hexagonal setting. As far as I know, the hexagonal setting of R32 (R32:H) is the first one that comes up in the ITvA as is listed a R32. The rhombohedral/primitive setting of R32 (R32:R) comes second in the ITvA, I guess the first setting takes precedence. H32 is a pdb/ccp4ism. In my cctbx-skewed view, it looks like this: R32 == R32:H (== H32; not supported by the cctbx) R32:R is the primitive setting of R32:H Appending the setting to the space group makes life easier (no ambiguities) and you can do more funky stuff if one has the stomach/need to do so [like P212121 (a+b,a-b,c) ]. HTHP Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] Retraction of 12 Structures
On Thu, 10 Dec 2009 13:06:36 -0600, Tanner, John J. tanne...@missouri.edu wrote: Some of you might be curious about the Ajees et al debacle that Jacob mentioned in his message. Here are two links: Nature Brief Communication that questioned the validity of one of Murthy's structures: http://www.nature.com/nature/journal/v448/n7154/full/nature06102.html Murthy's rebuttal: http://www.nature.com/nature/journal/v448/n7154/full/nature06103.html Jack I wrote up some disturbing parallels between the 2HR0 that was mentioned in the Nature communications and 2OU1 which is one of the twelve structures that were recently called into question. http://bit.ly/7QxbVg Sean
[ccp4bb] configuration or install issue with tk
Fellow users, I just installed v6.1.2 on Ubuntu 9.0.4 today and have run into the following problem when I try to run ccp4i for the first time as root to configure the program: r...@:/home//Documents# ccp4i No protocol specified Application initialization failed: couldn't connect to display :0.0 Error in startup script: can't read tk_version: no such variable ��� while executing catch set system(TK_VERSION) $tk_version ��� (file /usr/local/ccp4/ccp4-6.1.2/ccp4i/bin/ccp4i.tcl line 1) ��� (file /usr/local/ccp4/ccp4-6.1.2//bin/ccp4i line 1) The odd thing is that I can launch ccp4i just fine as a regular user, but then of course I get the message about the first time ccp4i has been run and the need to configure it, which requires administrator level access. Anyone have any ideas? Thanks, Stuart Endo-Streeter
Re: [ccp4bb] configuration or install issue with tk
Stuart, Are you logged-in as root or are you working in a root shell ( using su or sudo)? Depending on your security settings X-windows may not permit a program that is run from a root shell to access the display, which belongs to the user logged-in through X-windows. I get around the administrator access issue by installing CCP4, and all other non-OS software, with non-root ownership, a non-root administrator account, which shares the environment with all other users. For one thing, I do not want to source the multitude of /etc/csh.cshrc and .bashrc files as root. I am sure that others have different, and probably more elegant, solutions to this problem. PS. It also seems that the TCL/TK environment is not set in the root shell you are using. Good luck, Mark On Mon, 2009-12-14 at 16:51 -0600, Stuart Endostreeter wrote: Fellow users, I just installed v6.1.2 on Ubuntu 9.0.4 today and have run into the following problem when I try to run ccp4i for the first time as root to configure the program: r...@:/home//Documents# ccp4i No protocol specified Application initialization failed: couldn't connect to display :0.0 Error in startup script: can't read tk_version: no such variable while executing catch set system(TK_VERSION) $tk_version (file /usr/local/ccp4/ccp4-6.1.2/ccp4i/bin/ccp4i.tcl line 1) (file /usr/local/ccp4/ccp4-6.1.2//bin/ccp4i line 1) The odd thing is that I can launch ccp4i just fine as a regular user, but then of course I get the message about the first time ccp4i has been run and the need to configure it, which requires administrator level access. Anyone have any ideas? Thanks, Stuart Endo-Streeter Yours sincerely, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (409) 539-9138 Fax. (409) 747-4745 mailto://wh...@xray.utmb.edu http://xray.utmb.edu http://xray.utmb.edu/~white
Re: [ccp4bb] configuration or install issue with tk
With 'sudo' you should not have this issue. I agree, though, that having a separate user account to install crystallographic programs is quite an advantage from an administrative point of view. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Mon, 14 Dec 2009, Mark A. White wrote: Stuart, Are you logged-in as root or are you working in a root shell ( using su or sudo)? Depending on your security settings X-windows may not permit a program that is run from a root shell to access the display, which belongs to the user logged-in through X-windows. I get around the administrator access issue by installing CCP4, and all other non-OS software, with non-root ownership, a non-root administrator account, which shares the environment with all other users. For one thing, I do not want to source the multitude of /etc/csh.cshrc and .bashrc files as root. I am sure that others have different, and probably more elegant, solutions to this problem. PS. It also seems that the TCL/TK environment is not set in the root shell you are using. Good luck, Mark On Mon, 2009-12-14 at 16:51 -0600, Stuart Endostreeter wrote: Fellow users, I just installed v6.1.2 on Ubuntu 9.0.4 today and have run into the following problem when I try to run ccp4i for the first time as root to configure the program: r...@:/home//Documents# ccp4i No protocol specified Application initialization failed: couldn't connect to display :0.0 Error in startup script: can't read tk_version: no such variable while executing catch set system(TK_VERSION) $tk_version (file /usr/local/ccp4/ccp4-6.1.2/ccp4i/bin/ccp4i.tcl line 1) (file /usr/local/ccp4/ccp4-6.1.2//bin/ccp4i line 1) The odd thing is that I can launch ccp4i just fine as a regular user, but then of course I get the message about the first time ccp4i has been run and the need to configure it, which requires administrator level access. Anyone have any ideas? Thanks, Stuart Endo-Streeter Yours sincerely, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (409) 539-9138 Fax. (409) 747-4745 mailto://wh...@xray.utmb.edu http://xray.utmb.edu http://xray.utmb.edu/~white
Re: [ccp4bb] configuration or install issue with tk
I was running from a root shell. Ubuntu does not let me login as root. That is normally a good thing, but if I remember correctly to finish the ccp4i setup last time I on a CentOS system I had to login as root. I will try to reinstall tomorrow using sudo, but frankly I hate using it. Stuart -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Tim Gruene Sent: Monday, December 14, 2009 21:07 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] configuration or install issue with tk With 'sudo' you should not have this issue. I agree, though, that having a separate user account to install crystallographic programs is quite an advantage from an administrative point of view. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Mon, 14 Dec 2009, Mark A. White wrote: Stuart, Are you logged-in as root or are you working in a root shell ( using su or sudo)? Depending on your security settings X-windows may not permit a program that is run from a root shell to access the display, which belongs to the user logged-in through X-windows. I get around the administrator access issue by installing CCP4, and all other non-OS software, with non-root ownership, a non-root administrator account, which shares the environment with all other users. For one thing, I do not want to source the multitude of /etc/csh.cshrc and .bashrc files as root. I am sure that others have different, and probably more elegant, solutions to this problem. PS. It also seems that the TCL/TK environment is not set in the root shell you are using. Good luck, Mark On Mon, 2009-12-14 at 16:51 -0600, Stuart Endostreeter wrote: Fellow users, I just installed v6.1.2 on Ubuntu 9.0.4 today and have run into the following problem when I try to run ccp4i for the first time as root to configure the program: r...@:/home//Documents# ccp4i No protocol specified Application initialization failed: couldn't connect to display :0.0 Error in startup script: can't read tk_version: no such variable while executing catch set system(TK_VERSION) $tk_version (file /usr/local/ccp4/ccp4-6.1.2/ccp4i/bin/ccp4i.tcl line 1) (file /usr/local/ccp4/ccp4-6.1.2//bin/ccp4i line 1) The odd thing is that I can launch ccp4i just fine as a regular user, but then of course I get the message about the first time ccp4i has been run and the need to configure it, which requires administrator level access. Anyone have any ideas? Thanks, Stuart Endo-Streeter Yours sincerely, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (409) 539-9138 Fax. (409) 747-4745 mailto://wh...@xray.utmb.edu http://xray.utmb.edu http://xray.utmb.edu/~white
Re: [ccp4bb] configuration or install issue with tk
Mark A. White wrote: Stuart, Are you logged-in as root or are you working in a root shell ( using su or sudo)? Depending on your security settings X-windows may not permit a program that is run from a root shell to access the display, which belongs to the user logged-in through X-windows. Another way around this (assuming you have ssh server running) is login to a graphics desktop as yourself, then ssh r...@localhost Depending how your SSH, SSHD are configured, you may have to ssh -X or ssh -Y, but the X11 server will be available to the remote session so you can run ccp4i (or nedit or xclock or whatever X application), with copy and paste between the remote session window(s) and local, all without having to violate the taboo of never starting X as root. I get around the administrator access issue by installing CCP4, and all other non-OS software, with non-root ownership, a non-root administrator account, which shares the environment with all other users. This is also great for setting up crystallography for a number of workstations- install all the programs as a normal user on an nfs-mounted disk. Now whoever mounts that disk can source your master setup file and run the programs. Rather than installing as root in the usual /usr/local/bin/ or wherever, on every workstation. The actual system disks then just contain the operating system, which you can reinstall in a few hours (or less from an image) if they become corrupted or need to be updated to the latest distro. Stuart Endo-Streeter wrote: I was running from a root shell. Ubuntu does not let me login as root. That is normally a good thing, but if I remember correctly to finish the ccp4i setup last time I on a CentOS system I had to login as root. I will try to reinstall tomorrow using sudo, but frankly I hate using it. I don't think you need to reinstall- just open a terminal in your graphics desktop, ssh -X r...@localhost, verify that $DISPLAY is set and xclock works, then source ccp4.setup and run ccp4i. (could be wrong about that, though) Ed
Re: [ccp4bb] configuration or install issue with tk
On Mon, 14 Dec 2009, Edward A. Berry wrote: Mark A. White wrote: Stuart, Are you logged-in as root or are you working in a root shell ( using su or sudo)? Depending on your security settings X-windows may not permit a program that is run from a root shell to access the display, which belongs to the user logged-in through X-windows. Another way around this (assuming you have ssh server running) is login to a graphics desktop as yourself, then ssh r...@localhost Depending how your SSH, SSHD are configured, you may have to ssh -X or ssh -Y, but the X11 server will be available to the remote session so you can run ccp4i (or nedit or xclock or whatever X application), with copy and paste between the remote session window(s) and local, all without having to violate the taboo of never starting X as root. You have to ensure that X11Forwarding is set to 'yes' in /etc/ssh/sshd_config.
