Re: [ccp4bb] Difficult molecular replacement in R32 with pseudo translation
Andrei Lebedev has a program zanadu which you can access from: http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp it takes the solution and tries to sort out a spacegroup. Eleanor Jerry McCully wrote: Dear All: I got a problem with a data set in R32 space group with a resolution of 2.6. Pointless indicated that the space group was R32 and phenix triage showed that there was a pseudotranslation in the ASU. My protein is a hexamer and the matthew coeff. showed that there should just be two monomers in one ASU of R32. However, phaser in R32 and Molrep in R32 gave different solutions because Molrep used the pseudo-translation. I am not sure which one was correct because refinement of both solutions get stuck around 35% for Rfactor. I tried the molecular replacement in P1 and I got good solutions in Phaser. I think they are correct solutions because my protein was a hexamer and the crystal packing in P1 was formed by hexamers. How can I get correct solutions in R32 and finish the refinement? Many thanks in advance. Jerry McCully _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/171222985/direct/01/
Re: [ccp4bb] how to improve Rfree?
-Original Message- From: Vellieux Frederic [mailto:frederic.velli...@ibs.fr] Sent: 19 October 2009 19:31 To: Ian Tickle Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] how to improve Rfree? Hi Ian ( ccp4bb'ers), NCS ties reflections in reciprocal space by the interference G-function effect. Nothing more. So you get an R-free value that is lower than if you don't have NCS. One should be aware of that, and referees should be aware of that. Hi Fred That may be true (though not always), but I was actually referring to the problem of 'predicting' (usually after the fact!) what is the expected value of Rfree for an optimally refined structure, given Rwork (without knowing Rwork it's impossible!) and basic information about the data, the structure and the refinement protocol. This is (partly) a question of working out the observation/parameter ratio; then the big question arises as to how you count the NCS restraints. This calculation is tricky even in non-NCS cases, but as I said NCS really fouls things up (and I don't have a satisfactory solution)! Without having the expected value of Rfree as a basis for comparison how can you argue with the referees that the value of Rfree that you actually observed demonstrates that your model is free of bias or overfitting? My previous example of model bias in a 1 Ang isotropic B-factor refinement may have seemed remote and even irrelevant to many people struggling with 3 Ang data, but I would point out that model bias and the concomitant higher-than-expected Rfree is ubiquitous. If that were not true we wouldn't need to refine or model-build any MR solutions - just calculate structure factors and publish! The fact that Rfree never (well hardly ever) drops immediately to its final value but requires a lot of work model-building/refining is testament to the model bias still remaining in all the intermediate models between the initial MR model and the final refined structuure. Cheers -- Ian Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
[ccp4bb] Postdoctoral position at Carlsberg Laboratory
Applicants are invited for a post doctoral position at the Carlsberg Laboratory to study structure and activity of starch branching and debranching enzymes during barley grain filling and germination. The amount and quality of starch in barley are controlled by the enzymes involved in its biosynthesis; among them the branching (BE) and debranching enzymes (DBE). DBEs play an additional role during mashing/malting, since the fermentability of starch relies on this activity to degrade the α-1,6 branches of amylopectin. The aim of the present project is to characterize differences in BE and DBE activities in barley landraces during grain filling and germination and to seek to correlate these differences with exogenous proteins and with structural-functional properties of specific BE and DBE. Methods employed will include protein-protein interaction proteomics, enzymology, X-ray diffraction analysis of starch and protein. Our laboratory is fully equipped for all aspects of molecular biology, protein chemistry, protein crystallography and biophysical characterization of proteins. Applicants must have experience with proteomics, enzymology and/or biophysical characterization of proteins. Experience with production and purification of recombinant proteins will be considered an advantage. The position is a three-year position with one-year contract re-negotiation. Inquiries should be directed to: Anette Henriksen, E-mail: ane...@crc.dk. To apply, please send a CV including a brief description of research interests and accomplishments, and the names and addresses of two referees to: Anette Henriksen, Protein Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Copenhagen, Denmark E-mail: ane...@crc.dk The Protein Chemistry Group at Carlsberg Laboratory studies starch metabolism from a structural-biochemical perspective. The Laboratory was set up in Copenhagen 1875 by the founder of Carlsberg to develop a scientific basis for malting, brewing, and fermenting operations, and it has a long record in protein chemistry, yeast biology and plant physiology. -- Anette Henriksen, Prof., Ph.D. Carlsberg Laboratory, Biostructure Group, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark. Phone: +45 33275222. Fax: +45 33274765 This e-mail may contain confidential information and is intended solely for the addressee, and any use and disclosure of this information is strictly prohibited and may be unlawful. If you have received this e-mail by mistake, please notify us immediately and delete this e-mail without producing, distributing or retaining copies hereof. We believe, but do not warrant that this e-mail and any attachments, are virus free. You should take full responsibility for virus checking.
[ccp4bb] using -j option in fink during installation of ccp4 and coot
dear all, do somebody know where to tell fink to use multiple processors (e.g. make -j 9) during installation or update of big packages like ccp4 or coot ? thank you Özkan -- Özkan Yildiz, Dr. Max-Planck-Institute of Biophysics Department of Structural Biology Max-von-Laue-Str. 3 60438 Frankfurt email: oezkan.yil...@mpibp-frankfurt.mpg.de Office: +49-69-6303-3051 Lab:+49-69-6303-3013 Fax:+49-69-6303-2209
Re: [ccp4bb] crystallography teaching advice: f(S) ?
William G. Scott wrote: In my case at least, it isn't a question of failing to take an interest, but rather a complete sense of frustration when trying to communicate with people who insist on speaking utter jibberish. The point of the postmodernism generator website is to show just how mechanical, arbitrary, and ultimately how vacuous this stuff really can be. On a more serious level, we have the case of Sokal's Social Text Affair. Sokal is a physicist who published a paper in the prestigious journal Social Text entitled Transgressing the Boundaries: Toward a Transformative Hermeneutics of Quantum Gravity. The paper was a total spoof, but the editors and reviewers (none of which were qualified to pass judgement on quantum gravity) decided it was a great achievement and worthy of publication. Then when he admitted the hoax, all hell broke loose. cf: http://www.physics.nyu.edu/faculty/sokal/ Again, I'm afraid there is a problem here with the problematic overloading of the term 'postmodern'. I agree with everything you say concerning postmodern philosphy, the Sokal affair, the postmodernism generator, and so on. However, postmodernity as a description of the prevailing worldview in contemporary western culture is a completely different kettle of fish and requires *no* jargon to understand. None. However, there may also be a pond-difference at play here. Since one of the critiques of modernity which has driven postmodern relativism is the critique of colonialism, and in Europe (and particularly the UK) we tend to be aware of our role in some of the worse aspects of colonialism, then it seems plausible that European culture is more influenced by postmodern ideas than the US. A comparison of EU and US foreign policy over the last two decades (non-interventionism being shaped by relativism even in the face of genocide, versus interventionism shaped by the moral certainty of absolutism) would tend to support this view. If that is correct, then my advice to take postmodernity seriously (the sociology, not the philosophy), may be less relevant to you than to my European colleagues. However, I am not sufficiently in touch with the breadth of US culture to say for sure. I don't have time for a full exposition, but here's a couple of illustrations of changes which are taking place which have direct impact on science communication. In the UK at least, teaching strategies have changed to reflect the fact that appeals-to-authority no longer carry the weight they used to - school science involves more discovery based learning. Similarly, TV science documentaries no longer attempt to communicate facts, rather they tell stories, usually following the intellectual journey of a scientist of scientists in reaching a discovery. So, I agree with you, as scientists postmodern philosophy is useless to us. However, understanding postmodern society (at least in the EU, possibly in the US) can be extremely useful in communicating science effectively. Kevin p.s. Creationism is a confounding issue here, because it is on the rise in both the US and EU. However I think the sociological reasons for the rise of young earth creationism (which is notably absent from the Christian 'fundamentals' essays of the late 19thC from which the term fundamentalism comes) are fundamentally different in the US and in Europe.
Re: [ccp4bb] crystallography teaching advice: f(S) ?
On 20 Oct 2009, at 10:53, Kevin Cowtan wrote: I don't have time for a full exposition, but here's a couple of illustrations of changes which are taking place which have direct impact on science communication. In the UK at least, teaching strategies have changed to reflect the fact that appeals-to- authority no longer carry the weight they used to - school science involves more discovery based learning. Similarly, TV science documentaries no longer attempt to communicate facts, rather they tell stories, usually following the intellectual journey of a scientist of scientists in reaching a discovery. I thought that the point of Enlightenment science was a rejection of (Aristotelian) authority, basing science of empirical observations. If properly conducted, Science is inherently not based on authority but on evidence. Good school science teaching was always based on discovery (my first chemistry book was called Chemistry by discovery) It is true that coverage of science in popular media is generally poor Phil
[ccp4bb] NADP - ADP binding
Dear All Can any one mention some reference regarding the binding of NADPH or ADP in the surface of the protein. Is there any rules that dominate these two cofactors to select the surface istead of typical Rossmann fold. Thank you Sajid Yahoo! India has a new look. Take a sneak peek http://in.yahoo.com/trynew
Re: [ccp4bb] NADP - ADP binding
Michael Rossmann and colleagues did some work on the binding of fragments of cofactors to dogfish lactate dehydrogenase. In the 70's I think. Can be found on google scholar. Perhaps that's what you are after? Can't find the reference right now (it's in one of my drawers but I don't know which one...). I passed the reference on to Nicolas Coquelle @ualberta (coque...@ualberta.ca) a few days ago but that was from my home e-mail address so I don't have it here in the office. Fred. sajid akthar wrote: Dear All Can any one mention some reference regarding the binding of NADPH or ADP in the surface of the protein. Is there any rules that dominate these two cofactors to select the surface istead of typical Rossmann fold. Thank you Sajid Yahoo! India has a new look. Take a sneak peek http://in.yahoo.com/trynew attachment: Frederic_Vellieux.vcf
Re: [ccp4bb] NADP - ADP binding
This is a good start for Rossmann folds, I find. (I'm not sure if this is what you want though.) Chemical and biological evolution of a nucleotide-binding protein. Michael G. Rossmann, Dino Moras Kenneth W. Olsen. Nature Vol. 250 July 19 1974, p194. (Structural alignments in 1974 - wow!) If anyone has votes for other favourite papers of this ilk, I'm all ears! Mark 2009/10/20 Vellieux Frederic frederic.velli...@ibs.fr: Michael Rossmann and colleagues did some work on the binding of fragments of cofactors to dogfish lactate dehydrogenase. In the 70's I think. Can be found on google scholar. Perhaps that's what you are after? Can't find the reference right now (it's in one of my drawers but I don't know which one...). I passed the reference on to Nicolas Coquelle @ualberta (coque...@ualberta.ca) a few days ago but that was from my home e-mail address so I don't have it here in the office. Fred. sajid akthar wrote: Dear All Can any one mention some reference regarding the binding of NADPH or ADP in the surface of the protein. Is there any rules that dominate these two cofactors to select the surface istead of typical Rossmann fold. Thank you Sajid Yahoo! India has a new look. Take a sneak peek http://in.yahoo.com/trynew -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay, France. Tel: (33) 169157968 Fax: (33) 169853715 Skype: markabrooks
Re: [ccp4bb] crystallography teaching advice: f(S) ?
On Tue, 2009-10-20 at 11:45 +0100, Phil Evans wrote: On 20 Oct 2009, at 10:53, Kevin Cowtan wrote: I thought that the point of Enlightenment science was a rejection of (Aristotelian) authority, basing science of empirical observations. If properly conducted, Science is inherently not based on authority but on evidence... Indeed. The word expertise is more appropriate in science than authority. - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] TEACH-SG Workshop Advanced Strategies for the Expression of Proteins and Protein Complexes in Yeast Barcelona, November 19 20th, 2009
Spine 2-Complexes - Teach SG workshop: Advanced Strategies for the Expression of Proteins and Protein Complexes in Yeast Barcelona, Spain. November 19-20, 2009 Important notice: due to a technical error, online registration forms sent between October 1-13, 2009 may not have been received correctly. If you have registered for this event and have not received acknowledgment that your form was received, please visit the event webpage http://www.irbbarcelona.org/biomed/teachsg and resend your application. The workshop is aimed at advanced graduate students and postdoctoral fellows and will deal with state-of-the-art technologies for the expression of proteins and multisubunit protein complexes in yeast. Fundamentals, practical methods and illustrative examples for S. cerevisiae and P. pastoris will be presented in depth by expert speakers. Advantages of expression in yeast in comparison with other expression systems, such as E. coli, baculovirus-infected insect cells or mammalian cells, will be discussed. Deadline for registration extended to: October 31, 2009 Registration details at http://www.irbbarcelona.org/biomed/teachsg There is no registration fee for this conference, but the number of participants is limited to 25. Priority will be given to PhD students and postdoctoral fellows. All participants must submit a CV, and PhD students should also include a recommendation letter from their supervisor. Participants are also invited to submit abstracts for poster presentations, a number of which will be selected for short talks. Abstracts should include a title, authors, affiliations, summary (max 250 words) and references. Please see the workshop poster here http://www.irbbarcelona.org/files/File/poster-workshop-tech.pdf . For more information, please contact the Barcelona BioMed Secretariat at bio...@irbbarcelona.org
[ccp4bb] R-free/R and resolution analysis
Engin The PDBe provide a service to plot many different statistical properties in the PDB against other properties. The link is below. You can see that there is an option of RDiff which is the difference between R and R-Free for all structures that contain both data. Take a look at this first. There is a second parameter which you can set to resolution and this will allow you to draw a plot that you want. This will draw a 3D isometric plot which you can scale, and pick data points to view particular entries. http://www.ebi.ac.uk/pdbe-as/pdbestatistics/PDBeStatistics.jsp Regards Tom Oldfield Does anyone already have the PDB-wide R/Rfree gap versus resolution data (it does not seem that the PDB maintains one)? Ed. The friendly people in Uppsala has something here by the name Harry Plotter: http://xray.bmc.uu.se/gerard/supmat/eds/plotter.html This might be somewhat dated now. Engin
Re: [ccp4bb] NADP - ADP binding
Dear Sajid, there is a Gareth Stockwell's paper (from Janet Thornton's lab) that maps binding modes of ATP and NAD in known protein structures. It might help. http://www.ncbi.nlm.nih.gov/pubmed/16405908?ordinalpos=1itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PMID: 16405908 best wishes, --marian ## Marian Novotný Department of Cell Biology Faculty of Science Charles University in Prague Vinicna 7 Praha 2 12843 Czech Republic GPS: 50;4' 20.07N, 14;25'27.02E mail: mar...@natur.cuni.cz phone: +420221951769 ## On Oct 20, 2009, at 1:04 PM, sajid akthar wrote: Dear All Can any one mention some reference regarding the binding of NADPH or ADP in the surface of the protein. Is there any rules that dominate these two cofactors to select the surface istead of typical Rossmann fold. Thank you Sajid Yahoo! India has a new look. Take a sneak peek http://in.yahoo.com/trynew
Re: [ccp4bb] NADP - ADP binding
Sajid, It is not clear what you are asking. Are you asking whether there are common structural features in domains that bind nucleotide di/tri phosphates and dinucleotides? Or are there clear structural rules to consider when designing a (di)nucleotide binding site. If it is the former, then yes there are a whole class of enzymes/proteins that use a common motif design for binding (di)nucleotides. However, that being said, exceptions to these rules are also found. If you are asking about the latter, there are no clear rules, but structural considerations (how the nucleotide base is bound, the stereochemistry of the base to the ribose ring - syn or anti, how to ligand the ribose, etc.) that must be dealt with. But again, there are exceptions to these rules. Michael's seminal Nature paper did get everyone thinking about the issue of structure-function relationships (and yes we did structural superpositions back in 1970's on our trusty CDC 6600 with 60-bit words), proposing even the existence of a half Rossmann fold to bind nucleotides. However, even today, observing a Rossmann fold in a structure does not mean that the domain binds a dinucleotide, and a protein with no Rossmann fold can bind (di)nucleotides quite nicely. The latter situation is illustrated by these papers: Jin, Y. et al. Crystal structure of human type III 3alpha- hydroxysteroid dehydrogenase/bile acid binding protein complexed with NADP(+) and ursodeoxycholate. (2001) Biochemistry 40: 10161-10168 Putnam, C.D. et al. Active and inhibited human catalase structures: ligand and NADPH binding and catalytic mechanism. (2000) J.Mol.Biol. 296: 295-309 As suggested I would query Michael's papers from the 70's and 80's on the dehydrogenases: Eventoff and Rossmann. (1975) The evolution of Dehydrogenase and Kinases. CRC Crit. Rev. Biochem. 3, 111-140. Rossmann and Argos (1978) The Taxonomy of Binding Sites in Proteins. Molec. Cell. Biochem. 3(21), 161-182. These papers should give the information, from a historical and structural perspective, you need, from a historical and structural perspective, to begin your analysis. Regards, Michael R. Michael Garavito, Ph.D. Professor of Biochemistry Molecular Biology 513 Biochemistry Bldg. Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: garav...@msu.edu On Oct 20, 2009, at 7:42 AM, Mark Brooks wrote: This is a good start for Rossmann folds, I find. (I'm not sure if this is what you want though.) Chemical and biological evolution of a nucleotide-binding protein. Michael G. Rossmann, Dino Moras Kenneth W. Olsen. Nature Vol. 250 July 19 1974, p194. (Structural alignments in 1974 - wow!) If anyone has votes for other favourite papers of this ilk, I'm all ears! Mark 2009/10/20 Vellieux Frederic frederic.velli...@ibs.fr: Michael Rossmann and colleagues did some work on the binding of fragments of cofactors to dogfish lactate dehydrogenase. In the 70's I think. Can be found on google scholar. Perhaps that's what you are after? Can't find the reference right now (it's in one of my drawers but I don't know which one...). I passed the reference on to Nicolas Coquelle @ualberta (coque...@ualberta.ca) a few days ago but that was from my home e- mail address so I don't have it here in the office. Fred. sajid akthar wrote: Dear All Can any one mention some reference regarding the binding of NADPH or ADP in the surface of the protein. Is there any rules that dominate these two cofactors to select the surface istead of typical Rossmann fold. Thank you Sajid Yahoo! India has a new look. Take a sneak peek http://in.yahoo.com/trynew -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay, France. Tel: (33) 169157968 Fax: (33) 169853715 Skype: markabrooks
[ccp4bb] different Rfactors in different Refmac versions
Dear Ccp4 Users, I have refined a 2.3 A structure with Refmac in space group I4(1)22. Lately I had to switch from refmac version 5.2.0019 running on a Linux computer to refmac version 6.0.2 on a Windows Vista system. Refmac works fine but I’m a little concerned about the fact that R/Rfree/FOM became really worse from 19.5/25.7/80.0 (older version) to 21.5/27.3/77.1 (newer version) just by changing the refmac version. Also the correlation coefficients became worse. The overall temperature factor was significantly lower. I observed this also with another newer version on a Linux system. I strictly used the same protocol with TLS restrained refinement using Babinet scaling without changing anything in the structure. Are there other restraints for bonds etc. in the different versions leading to such differences? I would like to know what is going on. I would appreciate your help or any hints! Thank you in advance, Gesa -- Gesa Volkers Institut für Biochemie, Molekulare Strukturbiologie Felix-Hausdorff-Straße 4 17489 Greifswald
[ccp4bb] FW:postdoc position at MacCHESS
Dear all, Please see the following advertisement for a postdoc position at MacCHESS. Please respond to search-l...@cornell.edu. Kind regards, Natalie Zhao CCP4 Group = Post-doctoral Associate - Biological Small-Angle Solution Scattering Cornell High-Energy Synchrotron Source The Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron Source (MacCHESS) has an opening for a post-doctoral associate. Applicants should have a Ph.D. degree in a field relevant to structural biology. Preference will be given to those with experience in x-ray solution scattering on biological systems (SAXS and WAXS). The successful candidate will be expected to collaborate with visiting research groups collecting data at MacCHESS. Activities will include applying state-of-the art algorithms to BioSAXS data, modeling macromolecular complexes, or studying conformationally- variable regions of proteins. Experience in developing hardware and software for automation including microfluidics is also desirable. Located on an ivy-league university campus in picturesque upstate New York, the Cornell High-Energy Synchrotron Source (CHESS) serves a world-wide user base of structural biologists, chemists, physicists, and engineers. MacCHESS is an NIH-supported National Resource providing support for structural biology at CHESS. MacCHESS is a heavily team-oriented environment. Good clear communication skills are a must, including fluency in the English language. This position is a 1-year appointment, renewable for up to 3 years total, contingent upon availability of funds and employee performance. Please provide an application and arrange to have at least three letters of reference sent to: Dr. Marian Szebenyi, Chair Postdoctoral Associate Search Committee Newman Lab Cornell University Ithaca, NY 14853 USA Applications should include a cover letter, curriculum vita, a publication list, and a detailed summary of research experience and interests. Electronic submissions and inquiries may be addressed to search-l...@cornell.edu. Deadline for application is November 15, 2009. Starting date is negotiable. Cornell is an equal opportunity employer. -- Scanned by iCritical. MacCHESS Postdoc position 8_09.doc Description: MacCHESS Postdoc position 8_09.doc
[ccp4bb] ctruncate error (kind of)
Dear all, I'm converting intensities from scala to amplitudes with ctruncate like so: ctruncate -mtzin scala_protein_3_001_180.mtz -colin /*/*/[IMEAN,SIGIMEAN] The data are native. An mtz file is generated, and it looks ok, but ctruncate doesn't terminate properly. Instead, after Anisotropy analysis, the following error is reported: CCP4 library signal mtz:No architecture information in file. (Warning) raised in MtzGet CCP4 library signal mtz:File not identified as MTZ (Error) raised in MtzGet Segmentation fault This happens with ctruncate in ccp4 6.1.0 and with ctruncate downloaded from ftp://ftp.ccp4.ac.uk/nds/bin/ctruncate, both on RHEL 5.4. Should I be concerned? Andreas === Andreas Förster Macromolecular Structure and Function Imperial College London
Re: [ccp4bb] ctruncate error (kind of)
Looks like a problem with your file. Can you try: od -a scala_protein_3_001_180.mtz | head If your file is an mtz file, you should get output starting a bit like this: 000 M T Z sp ! o etx nul D A nul nul nul nul nul nul If that is OK, then try: strings scala_protein_3_001_180.mtz | tail -1 If you file has not be truncated, you should see the full MTZ headers of the file. Kevin Andreas Forster wrote: Dear all, I'm converting intensities from scala to amplitudes with ctruncate like so: ctruncate -mtzin scala_protein_3_001_180.mtz -colin /*/*/[IMEAN,SIGIMEAN] The data are native. An mtz file is generated, and it looks ok, but ctruncate doesn't terminate properly. Instead, after Anisotropy analysis, the following error is reported: CCP4 library signal mtz:No architecture information in file. (Warning) raised in MtzGet CCP4 library signal mtz:File not identified as MTZ (Error) raised in MtzGet Segmentation fault This happens with ctruncate in ccp4 6.1.0 and with ctruncate downloaded from ftp://ftp.ccp4.ac.uk/nds/bin/ctruncate, both on RHEL 5.4. Should I be concerned? Andreas === Andreas Förster Macromolecular Structure and Function Imperial College London
[ccp4bb] FPLC for sale
---BeginMessage--- Dear All: Please see attached is an ad for our AKTAprime plus FPLC system which is only 2 years old, used a dozen times and in excellent condition. Thanks, Natalie Roy FPLC for sale.doc Description: MS-Word document ---End Message---
[ccp4bb] cofactor fragments and NADH binding (Rossmann) fold
Sorry about starting a new thread (this is not a new thread in fact but I mistakenly erased all the relevant ccp4bb messages). for dogfish LDH and binding of cofactor fragments see J Mol Biol. 1973 Jun 5;76(4):503-518. Fred.
[ccp4bb] Two Equally Good MR Solutions Found by Phaser
Dear Crystallographers, We got a highly repetitive dimeric protein solved by SeMet-SAD in P21 crystal form, and I am now trying to solve a dataset collected from a non-reproducible orthorhombic crystal of the same protein using the structure refined from P21 data. From the Scala statistics, the orthorhombic crystal diffracted to 2.2Å with an I/sigma of 3.1 at outmost shell; 98% complete overall, 89% complete 43.4-7.0Å, 99% complete 2.32-2.2Å, no twinning was detected. Due to the incompleteness at low resolution, it was hard to determine which orthorhombic space group it is in so data was scaled in P222. Very strong pseudo-translational symmetry has been detected by self-Patterson, as shown for reindexed data P21212 (space group later found by Phaser): Order No. Site Height/RmsGrid Fractional coordinates Orthogonal coordinates 111 128.24 0 0 0 0. 0. 0. 0.00 0.00 0.00 2 13 13 57.5160 44 38 0.5000 0.2741 0.500044.37 31.88 27.55 322 33.75 0 7 0 0. 0.0414 0. 0.00 4.82 0.00 4 14 14 16.0960 50 38 0.5000 0.3150 0.500044.37 36.63 27.55 5 12 12 15.7560 37 38 0.5000 0.2324 0.500044.37 27.03 27.55 633 12.28 0 13 0 0. 0.0836 0. 0.00 9.72 0.00 7 1507.0660 57 38 0.5000 0.3574 0.500044.37 41.56 27.55 8446.18 0 72 0 0. 0.4503 0. 0.00 52.36 0.00 9995.68 5 0 5 0.0410 0. 0.0683 3.64 0.00 3.76 10555.36 2 20 2 0.0142 0.1254 0.0206 1.26 14.59 1.14 11 11 115.3358 31 38 0.4852 0.1909 0.500043.06 22.20 27.55 12663.98 5 0 2 0.0435 0. 0.0286 3.86 0.00 1.58 13773.82 2 27 3 0.0168 0.1659 0.0334 1.49 19.30 1.84 14883.68 0 0 5 0. 0. 0.0722 0.00 0.00 3.98 15 10 103.4160 64 37 0.5000 0.4007 0.487244.37 46.59 26.84 Phaser was used to test all possible alternative space groups to find MR solution using the structure from P21 data: # Phaser_P222_MosFLM_all_spacegroup SPACegroup HALL P 2bc 2 #P 2 21 21 SOLU SET RFZ=9.1 TFZ=24.3 PAK=0 LLG=2545 LLG=3718 SOLU 6DIM ENSE ensemble1 EULER 273.0971.162 88.144 FRAC -0.03394 0.50659 -0.22125 SOLU SET RFZ=9.1 TFZ=25.0 PAK=0 LLG=2496 LLG=3622 SOLU 6DIM ENSE ensemble1 EULER 91.4910.850 89.812 FRAC 0.03435 -0.00618 0.00352 and it found 2 solutions with very similar Z-scores and LLG gains, If I am right they are not crystallographic equivalent, and Phaser checks that as well. I reindexed the data to P21212 and Phaser found the same solutions: # Phaser_Reindexed_P21212_2_solutions SPACegroup HALL P 2 2ab #P 21 21 2 SOLU SET RFZ=10.0 TFZ=23.0 PAK=0 LLG=3266 LLG=3718 SOLU 6DIM ENSE ensemble1 EULER 88.843 90.0631.249 FRAC -0.00661 -0.22126 -0.46598 SOLU SET RFZ=9.9 TFZ=23.2 PAK=0 LLG=3178 LLG=3624 SOLU 6DIM ENSE ensemble1 EULER 270.841 89.977 181.339 FRAC -0.50634 -0.00350 0.46533 The difference between the two solutions seems to be that the second solution translated along the longer 21 axis by about ~32Å, I chose the first solution to re-build and refine, and final R/Rfree I got was 21.6%/26.5%. After that, I hope to solve the ambiguity of which MR solution is right by running Phaser again with the complete model (including H2O): # Phaser_Reindexed_P21212_2_solutions SPACegroup HALL P 2 2ab #P 21 21 2 SOLU SET RFZ=12.8 TFZ=28.4 PAK=0 LLG=6542 LLG=7649 SOLU 6DIM ENSE ensemble1 EULER 180.1560.0000.000 FRAC -0.50060 -0.00065 0.49998 SOLU SET RFZ=12.8 TFZ=32.3 PAK=0 LLG=6036 LLG=7059 SOLU 6DIM ENSE ensemble1 EULER 179.201 180.0000.000 FRAC 0.00227 0.22262 -0.50054 It seems that the previous first solution has become the second solution, while the previous second solution became the first. Refmac refinement was performed on both solutions (H2O removed) came out from Phaser, solution 1 R/Rfree = 24.1/28.9 solution 2 R/Rfree = 24.8/28.7 the previous first solution got slightly worse scores, however, the R-factors for both solutions are so similar and both of them gave very similar electron density that I can not figure out which one is the right solution. I would very grateful for any advices. Thanks in advance, -- Xiaoli Xiong PhD Candidate Department of Cellular and Molecular Medicine School of Medical Sciences University of Bristol University Walk Bristol BS8 1TD, UK x.l.xi...@bristol.ac.uk
Re: [ccp4bb] crystallography teaching advice: f(S) ?
Interesting discussion by authoritative and expert CCP4BB contributors. Francis Bacon is often cited as one of the originators of enlightenment science. An recent (1964!) update on his methods can be found in http://pages.cs.wisc.edu/~markhill/science64_strong_inference.pdf. I think this still contains relevant material for anyone teaching science (including crystallography). Some interpretations of quantum mechanics (e.g. the influence of the observer on the observation) have provided encouragement for a postmodern philosophy of science. Until an agreed interpretation of quantum phenomena is obtained I think this will still be an issue. I am not sure what a post modern philosopher would make of the recent proposal (from two authoritative sources) that the time travelling Higgs Boson is sabotaging the LHC (it also apparently stopped the US Congress from funding the Superconducting Supercollider). Now I wish we could use this sort of excuse for why our synchrotrons have problems or why they are not funded. Colin -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of David J. Schuller Sent: 20 October 2009 13:44 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] crystallography teaching advice: f(S) ? On Tue, 2009-10-20 at 11:45 +0100, Phil Evans wrote: On 20 Oct 2009, at 10:53, Kevin Cowtan wrote: I thought that the point of Enlightenment science was a rejection of (Aristotelian) authority, basing science of empirical observations. If properly conducted, Science is inherently not based on authority but on evidence... Indeed. The word expertise is more appropriate in science than authority. - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] Two Equally Good MR Solutions Found by Phaser
Hello there, Don't you have extinctions along the axes allowing you to distinguish between the possible space groups? Or are the reflections along the reciprocal axes missing from the data set you have collected? Normally this is how one decides on the space group in orthorhombic 222, by checking the systematic absences. [is Nathan Zaccai in your institute? If so give him my regards] Fred. Message du 20/10/09 22:02 De : X Xiong, Cellular Molecular Medicine A : CCP4BB@JISCMAIL.AC.UK Copie à : Objet : [ccp4bb] Two Equally Good MR Solutions Found by Phaser Dear Crystallographers, etc etc
Re: [ccp4bb] NADP - ADP binding
Hello, I'm not entirely sure I know what you mean, but what came to my mind was malic enzyme. Check out Liang Tong's summary of structural data: http://como.bio.columbia.edu/tong/Research/me.html This protein has 2 nucleotide binding sites, one in a canonical Rossman fold and another on the surface that is believed to be an allosteric site. However, I could be remembering this story wrong. --Paul --- On Tue, 10/20/09, Mark Brooks mark.bro...@u-psud.fr wrote: From: Mark Brooks mark.bro...@u-psud.fr Subject: Re: [ccp4bb] NADP - ADP binding To: CCP4BB@JISCMAIL.AC.UK Date: Tuesday, October 20, 2009, 7:42 AM This is a good start for Rossmann folds, I find. (I'm not sure if this is what you want though.) Chemical and biological evolution of a nucleotide-binding protein. Michael G. Rossmann, Dino Moras Kenneth W. Olsen. Nature Vol. 250 July 19 1974, p194. (Structural alignments in 1974 - wow!) If anyone has votes for other favourite papers of this ilk, I'm all ears! Mark 2009/10/20 Vellieux Frederic frederic.velli...@ibs.fr: Michael Rossmann and colleagues did some work on the binding of fragments of cofactors to dogfish lactate dehydrogenase. In the 70's I think. Can be found on google scholar. Perhaps that's what you are after? Can't find the reference right now (it's in one of my drawers but I don't know which one...). I passed the reference on to Nicolas Coquelle @ualberta (coque...@ualberta.ca) a few days ago but that was from my home e-mail address so I don't have it here in the office. Fred. sajid akthar wrote: Dear All Can any one mention some reference regarding the binding of NADPH or ADP in the surface of the protein. Is there any rules that dominate these two cofactors to select the surface istead of typical Rossmann fold. Thank you Sajid Yahoo! India has a new look. Take a sneak peek http://in.yahoo.com/trynew -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay, France. Tel: (33) 169157968 Fax: (33) 169853715 Skype: markabrooks
Re: [ccp4bb] Two Equally Good MR Solutions Found by Phaser
Hi, Thanks for all the replies. Paul said the two solutions are the same by crystallographical symmetry, does that mean the origin of the unit cell has changed and P21212 can have arbitrary origin of the cell along the b-axis? As I have generated the symmetry related pairs from each solution in Coot, they do not overlap each other but partly clashed into each other along the b-axis. Another question is I thought Phaser can automatically prune the solutions that are cryptographically the same (as suggested in its log file ), did Phaser fail that in my case? For the comments on incompleteness at low resolution, I thought it was crystal mounting problem, there was no overloads as crystal is tiny and diffracted weakly, but it is very strange that two of the axes are very incomplete at low resolution, I don't know any explanation for that, and due to the incompleteness at low res, systematic absences can not be observed, so space group can not determined by looking at them. Thank for all the advices so far, and I would like more suggestions to clarify my doubts. cheers -- Xiaoli Xiong PhD Candidate Department of Cellular and Molecular Medicine School of Medical Sciences University of Bristol University Walk Bristol BS8 1TD, UK x.l.xi...@bristol.ac.uk
Re: [ccp4bb] Colored proteins :)
Hi, One I remember (did my Ph.D. on it at the end of the 80s under the supervision of J. Drenth W. Hol) is quinoprotein methylamine dehydrogenase. Also, the old yellow enzyme, photoactive yellow protein and I am sure there are plenty others. Fred. Message du 21/10/09 02:25 De : Artem Evdokimov A : CCP4BB@JISCMAIL.AC.UK Copie à : Objet : [ccp4bb] Colored proteins :) Hello CCP4 folks! I have a quick question - could you suggest a few naturally intensely colored proteins? Colors based on small molecule co-factors (i.e. metal ions, flavonoids, etc.) are perfectly fine for my needs :) I already looked into GFP and its relatives, (bacterio)rodopsin, azurins/pseudoazurins, and hemoglobins - but I would appreciate more examples. I am sure there's a nice review out there somewhere but so far I've not found it. Thank you, Artem
