- phenixbb - phenix-online.org

Re: [phenixbb] Hardward phenix.refine
by Kay Diederichs 12 Apr '16

12 Apr '16

Colin, check out the first option in the FAQ at https://www.phenix-online.org/documentation/faqs/refine.html A core i7 and a Xeon of the same generation are equally fast if their frequency is the same. The main differences are that - Xeon E3 supports ECC memory (most core i* don't) - Xeon E5 supports Dual-CPU (core i* is just one) - Xeon E7 supports multi-CPU and is very expensive - most Xeons don't have built-in graphics whereas most core i* do There are many other small differences but most of them irrelevant; inspect the Wikipedia pages! Xeons won't be faster with phenix.refine; a core i7 already has enough cores - to increase their usage you'll have to recompile as per the FAQ. HTH, Kay > > Message: 1 > Date: Mon, 11 Apr 2016 07:56:39 +0000 > From: Colin Levy <C.Levy(a)manchester.ac.uk> > To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Hardward phenix.refine > Message-ID: <773C4580-FA01-4246-86E9-2D73AFD98421(a)manchester.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > Dear all, > > Having read the FAQ regarding hardware I have a few ideas but would greatly appreciate any input from the community or developers. > > Would anyone like to suggest the best configuration of hardware for running phenix.refine? I mainly operate in OSX but have no issue with switching operating system if I can get a faster setup. My current thoughts are either something running a 4GHz Quad core i7 or an alternative would be a 3.7GHz Quad-Core Intel Xeon E5 (iMac v Mac Pro) or equivalent Linux builds. > > I know that the i7 is reasonably fast as I have this setup in a different machine and phenix.refine runs reasonably quickly but as ever I would like it to be faster. Budget is not unlimited by any means but I would be interested in learning what an optimal setup might look like. > > Many thanks, > > Colin > > > Manchester > Protein > Structure > Facility > > Dr. Colin W. Levy > MIB G034 > Tel. 0161 275 5090 > Mob.07786 197 554 > c.levy(a)manchester.ac.uk<mailto:[email protected]> > > Manchester Institute of Biotechnology | University of Manchester | 3.020 Garside Building | 131 Princess Street | Manchester | M1 7DN

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Re: [phenixbb] Phenix Xtriage label error
by Alex Lee 12 Apr '16

12 Apr '16

Hi Dorothee and Billy, Thank you for your information! I have both I, SIGI and IPR, SIGIPR labels in my unmerged MTZ (I checked this with ViewHKL). But it seems the Xtriage only offers choices to merged mtz. I tried to choose I,SIGI, Merged option (even though my mtz is unmerged), the Xtriage output shows "anomalous flag false" and I did not get any additional anomalous information from the report. On Tue, Apr 12, 2016 at 12:16 PM, Dorothee Liebschner <dcliebschner(a)lbl.gov> wrote: > Hi Alex, > > What data labels are in the file pointless_xxx.mtz? > You can check with > > phenix.mtz.dump pointless_xxx.mtz > The output should list the available labels. > (you should see the labels also in hklview) > > You cannot leave the data labels choice blank in xtriage, as you have two > data choices in your file, so you need to tell the program which ones to > use. > > Apart from xtriage, it is always helpful to check the anomalous signal > reported in various log files from your data processing steps, such as > aimless.log and also from mosflm (I am not familiar to mosflm but I guess > it outputs also some info about anomalous signal?). > > Best wishes, > > Dorothee > > > > > > On Tue, Apr 12, 2016 at 11:08 AM, Alex Lee <alexlee198609(a)gmail.com> > wrote: > >> Dear Phenixbb members, >> >> I have a data-set of a 8 kDa protein crystal around 2.5A resolution. The >> protein crystal was soaked in potassium iodine before collecting data using >> in-house beam (1.54A wavelength). As I expected some anomalous signal from >> the iodine ion from the crystal, after I use Imosflm to index, integrate >> and scale the data (space group P3). I got four output .mtz files: >> pointless_XXX.mtz; aimless_xxx.mtz; ctruncate_xxx.mtz; >> ctruncate_xxx-unique.mtz. After I check with viewHKL, I found the only >> unmerged mtz data is pointless_XXX.mtz, the other three mtz files are >> merged. >> >> The next step I tried to use Phenix Xtriage (Linux version 1.10.1) to >> check my mtz data for anomalous completeness, I thought in this step my mtz >> should be unmerged type to see the anomalous signal, so I chose >> "pointless_xxx.mtz" as Xtriage input, but for the data labels in the >> Xtriage GUI panel, I can only have two choices of "I, SIGI, Merged" and >> "IPR, SIGIPR, Merged", it seems I do not have a choice of an unmerged mtz >> label. I decide to leave this choice blank by choosing data labels"---". >> After I click "run", Xtriage gave an error "please select labels for input >> data". >> >> Any input on this issue? >> >> Thanks in advance. >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > >

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Phenix Xtriage label error
by Alex Lee 12 Apr '16

12 Apr '16

Dear Phenixbb members, I have a data-set of a 8 kDa protein crystal around 2.5A resolution. The protein crystal was soaked in potassium iodine before collecting data using in-house beam (1.54A wavelength). As I expected some anomalous signal from the iodine ion from the crystal, after I use Imosflm to index, integrate and scale the data (space group P3). I got four output .mtz files: pointless_XXX.mtz; aimless_xxx.mtz; ctruncate_xxx.mtz; ctruncate_xxx-unique.mtz. After I check with viewHKL, I found the only unmerged mtz data is pointless_XXX.mtz, the other three mtz files are merged. The next step I tried to use Phenix Xtriage (Linux version 1.10.1) to check my mtz data for anomalous completeness, I thought in this step my mtz should be unmerged type to see the anomalous signal, so I chose "pointless_xxx.mtz" as Xtriage input, but for the data labels in the Xtriage GUI panel, I can only have two choices of "I, SIGI, Merged" and "IPR, SIGIPR, Merged", it seems I do not have a choice of an unmerged mtz label. I decide to leave this choice blank by choosing data labels"---". After I click "run", Xtriage gave an error "please select labels for input data". Any input on this issue? Thanks in advance.

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Hardward phenix.refine
by Colin Levy 11 Apr '16

11 Apr '16

Dear all, Having read the FAQ regarding hardware I have a few ideas but would greatly appreciate any input from the community or developers. Would anyone like to suggest the best configuration of hardware for running phenix.refine? I mainly operate in OSX but have no issue with switching operating system if I can get a faster setup. My current thoughts are either something running a 4GHz Quad core i7 or an alternative would be a 3.7GHz Quad-Core Intel Xeon E5 (iMac v Mac Pro) or equivalent Linux builds. I know that the i7 is reasonably fast as I have this setup in a different machine and phenix.refine runs reasonably quickly but as ever I would like it to be faster. Budget is not unlimited by any means but I would be interested in learning what an optimal setup might look like. Many thanks, Colin Manchester Protein Structure Facility Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 c.levy(a)manchester.ac.uk<mailto:[email protected]> Manchester Institute of Biotechnology | University of Manchester | 3.020 Garside Building | 131 Princess Street | Manchester | M1 7DN [cid:[email protected]]<https://www.facebook.com/MIB2006/?ref=aymt_homepage_panel>[cid:[email protected]]<https://plus.google.com/u/0/b/111834792186886067949/111834792186886067949/p…>[cid:[email protected]]<https://www.linkedin.com/company/manchester-institute-of-biotechnology?trk=…>[cid:[email protected]]<https://twitter.com/?lang=en-gb&lang=en-gb>[cid:[email protected]]<https://www.youtube.com/channel/UCCBV8zDxk4L9yOEcujvSFNw> <https://www.youtube.com/channel/UCCBV8zDxk4L9yOEcujvSFNw><https://plus.google.com/u/0/b/111834792186886067949/111834792186886067949/p…><https://plus.google.com/u/0/b/111834792186886067949/111834792186886067949/p…><https://plus.google.com/u/0/b/111834792186886067949/111834792186886067949/p…>

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Call for targets for CASP12 - Critical Assessment of Protein Structure Prediction
by Torsten Schwede 08 Apr '16

08 Apr '16

Dear colleagues, The CASP experiment is looking for prediction targets: Novel folds, membrane proteins, protein complexes and multimers, comparative modeling targets. As many of you know, the CASP community experiments have been running once every two years since 1994, collecting information on soon to be solved structures from the experimental community, and passing on sequence data to the structure modeling community so that blind predictions of structure can be collected and assessed. Over that period CASP has seen enormous progress in the quality of modeled structures, but many problems remain, and further testing of prediction methods is imperative for advancing the field. CASP organizers collect target information for a three month season every two years, and in that period we can acquire around 100 targets, sufficient to evaluate the state of the art for most types of modeling. For those of you who have not provided targets to CASP before, the procedure is simple - there is a web page for submitting targets, and a very experienced staff to deal with any queries. We don't need the structure in advance of its release by the PDB, and if we are notified early enough (a minimum of three weeks before release, more is better) there need be no delay in structure release. We need all sorts of targets and in general everything that has low coverage by the templates (<70% of the sequence length) and relatively low sequence identity to the best template (<50% ) will be appreciated. In particular, we are interested in: 1. Novel folds and membrane protein targets. Last round we observed some interesting methods developments for contact prediction and ab initio modeling, and it is important to be able to decisively evaluate their effectiveness this CASP again. 2. Protein complexes and multimers. Since the last edition of CASP, the assessment of structure prediction methods has stronger emphasis on evaluating the accuracy of quaternary structure prediction. Both oligomeric targets and complexes are of interest for the experiment. 3. A diversity of comparative modeling targets. Cases where there is fairly high sequence identity (30-50%) between the target structure and an available template are valuable for testing the degree to which model accuracy can approach that of experiment, particularly in functionally critical regions. Cases with lower sequence identity to template, right down to undetectable, are valuable for testing the ability of the methods to detect remote homologs, to overcome challenging alignment difficulties, to make use of multiple templates, and to build regions of the structure not obviously available from a template. The time table is similar to previous CASPs: The prediction season opens at the beginning of May, and will run until the end of July. We are releasing targets continuously throughout that period, as evenly spaced as possible, aiming for about 100 targets altogether. Each target will be available for prediction for a period of three weeks. For cases where longer periods are possible, these targets may be used to test refinement and data-assisted methods. It is of course important that there not be any kind of public release of the experimental structure (including things like pictures on web pages or abstracts) until after the predictions for that target are closed. As many of you know, it's fairly simple, with just two things to bear in mind. First, because of the timing framework, there needs to be at least a month between the submission date and any release of the structure. Second, we ideally need the experimental co-ordinates by the beginning of August and definitely by the end of August, so that the predictions can be assessed. At that point, they can be kept confidential if necessary, though we would like to provide them to predictors of your structure at the beginning of November at the latest, so that can see how well they have done. Participants would also usually like to be able to show slides and discuss their predictions at the meeting at the beginning of December. So, if you are currently working on an interesting protein structure suitable as prediction target for CASP , we would be most grateful if you would inform us via the target entry page: http://www.predictioncenter.org/casp12/targets_submission.cgi After CASP prediction season is over we usually publish a paper on the experimentalists' insights into the most interesting targets (see below). 2015: Some of the most interesting CASP11 targets through the eyes of their authors. Kryshtafovych A, Moult J, Baslé A, Burgin A, Craig TK, Edwards RA, Fass D, Hartmann MD, Korycinski M, Lewis RJ, Lorimer D, Lupas AN, Newman J, Peat TS, Piepenbrink KH, Prahlad J, van Raaij MJ, Rohwer F, Segall AM, Seguritan V, Sundberg EJ, Singh AK, Wilson MA, Schwede T. Proteins. 2015 Oct 16. doi: 10.1002/prot.24942. [Epub ahead of print]. PMID: 26473983. 2014: Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg O, Lorimer D, Luecke H, Ma X, Nelson DC, van Raaij MJ, Rohwer F, Segall A, Seguritan V, Zeth K, Schwede T. Proteins. 2014 Feb;82 Suppl 2:26-42. doi: 10.1002/prot.24489. Erratum in: Proteins. 2015 Jun;83(6):1198. PMID: 24318984. 2011: Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. Kryshtafovych A, Moult J, Bartual SG, Bazan JF, Berman H, Casteel DE, Christodoulou E, Everett JK, Hausmann J, Heidebrecht T, Hills T, Hui R, Hunt JF, Seetharaman J, Joachimiak A, Kennedy MA, Kim C, Lingel A, Michalska K, Montelione GT, Otero JM, Perrakis A, Pizarro JC, van Raaij MJ, Ramelot TA, Rousseau F, Tong L, Wernimont AK, Young J, Schwede T. Proteins. 2011;79 Suppl 10:6-20. doi: 10.1002/prot.23196. Epub 2011 Oct 21. PMID: 22020785. Thanks, CASP organizing committee: John Moult, University of Maryland, USA Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis, USA Torsten Schwede, University of Basel, Switzerland Anna Tramontano, University of Rome, Italy Get in touch: casp(a)predictioncenter.org<mailto:[email protected]> More information: http://www.predictioncenter.org/casp12/index.cgi Submit a target: http://www.predictioncenter.org/casp12/targets_submission.cgi

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Position available with Phaser team at University of Cambridge
by Randy Read 06 Apr '16

06 Apr '16

I’d like to draw your attention to an opening that we have for someone to join the team developing Phaser. The ideal person would have experience with C++ and/or Python, graphical interfaces, and knowledge of how macromolecular structures are solved and validated, but it would also be good to hear from people who only tick some of those boxes. Full details of the position and the application process are given on the jobs.ac.uk website: http://www.jobs.ac.uk/job/ANJ468/research-associate/. I’m happy to answer any informal enquiries about the position. Best wishes, Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Modeller- homology modelling
by Shilpa Janarthanan 03 Apr '16

03 Apr '16

Hello, Has anyone encountered this error while running Modeller for doing Homology modelling "Sequence mismatch between alignment and pdb"? If yes, how did you solve it? I checked, there is no mismatch between sequence(both fasta and pdb) and alignment. Thank you. -- Shilpa J Bioinformatics Dept., SASTRA University.

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Finding the transcript
by Shilpa Janarthanan 02 Apr '16

02 Apr '16

Hello, Can you tell me, on what basis should I find the exact transcript (mRNA) sequence for a given protein sequence, in NCBI -Gene? Thank you. -- Shilpa J Bioinformatics Dept., SASTRA University.

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The Hitchhiker’s Guide to the Biomolecular Galaxy symposium - May 11-12th 2016
by Noinaj, Nicholas 02 Apr '16

02 Apr '16

Dear PHENIXbb, I would like to bring to your attention our upcoming symposium (May 11-12) hosted here at Purdue University for students and postdocs. There will also be a Career Session on May 10th for students and postdocs only. More information is listed below and can also be accessed on our website: Symposium Website: https://purduegalaxy.science.purdue.edu/ Symposium Flyer: https://purduegalaxy.science.purdue.edu/images/2016/hg2bg_logo_Flyer_new.jpg Registration (including breakfast and lunch for both days and a T-shirt!) and abstract submission are completely FREE! And now, we are offering at least 10 travel grants (up to $150 each) for students and postdocs who are within driving distance of Purdue. Please forward this to anyone you think might be interested. Thanks in advance! Cheers, Nick Nicholas Noinaj 240 S. Martin Jischke Dr. Hockmeyer Building of Structural Biology, Rm 333 Dept. of Biological Sciences, Purdue Univ. West Lafayette, IN 47907 765-496-0061 (office) 765-496-0059 (wetlab) nnoinaj(a)purdue.edu ++++++++ Greetings all from Purdue! We would like to cordially invite you, your colleagues, students, postdocs and staff to our upcoming symposium hosted here at Purdue University, West Lafayette campus. The name of the symposium is: The Hitchhiker’s Guide to the Biomolecular Galaxy symposium May 11-12, 2016 ARMS 1010, Purdue University The symposium will highlight research from students and postdocs from neighboring institutions and from many departments here at Purdue including Biological Sciences, Medicinal Chemistry and Molecular Pharmacology, Chemistry, Biochemistry, and Physics and Astronomy. The keynote speaker will be Dr. Peter Kwong from NIAID/NIH who will talk about his work on ‘Multi-dimensional searching and the coordinates of effective HIV-1 and RSV vaccines’. In addition to the keynote address, the symposium will include six scientific sessions covering the following topics: Disease, Pathogenesis and Therapeutics; Biosynthesis and Catalysis; Biophysical Methods and Emerging Techniques; Macromolecular Assemblies and Complexes; and Disorder and Conformational Plasticity. There will also be opportunities for discussion and interactions during catered breaks, a poster session, and a reception. And back by popular demand, a Career Session will also be hosted on the evening of May 10th at the Lafayette Brewing Company for students and postdocs and will include a panel representing industry, academia, and government. Registration and abstract submission are both FREE. Undergraduates, graduates, and postdocs are encouraged to submit abstracts for poster or oral presentations. Prizes for best posters (undergrad ($100), grad ($150), and postdoc($150)) and oral presentations (grad ($200) and postdoc ($200)) will also be awarded at the close of the symposium. REGISTER NOW for the HG2BG symposium!!! The deadline is quickly approaching!!! Click link below to Register (Abstract submission NOT required!): https://purdue.qualtrics.com/jfe/form/SV_eeZ2HT409liD27z Just LOOK at ALL the FREE stuff you get with registration: Just a 1-click, 1-minute process FREE registration fees! FREE abstracts submission! FREE attendance to the Career Session which includes food and drinks at Lafayette Brewing Company! FREE HG2BG symposium T-shirt! FREE chance to win either a poster/oral presentation prize ($100-$200 each)! FREE food and drinks at the poster presentations/reception! FREE breakfast for both days of the symposium! FREE lunch for both days of the symposium! FREE travel grants for up to $150 each for registrants from neighboring institutions (10 available)! FREE attendance to all poster and oral presentations, including talk by Peter Kwong! We look forward to your participation and another successful symposium! On behalf of the organizing committee: Satarupa Bhaduri (Biological Sciences) Chen Chen (Medicinal Chemistry and Molecular Pharmacology) Samantha Lee (Biochemistry) Ngango Yvon Rugema (Chemistry) Phillip Rushton (Biological Sciences/ PULSe) Valentyn Stadnytskyi (Physics and Astronomy) Dr. Nicholas Noinaj (Faculty advisor; Biological Sciences) A special thanks to our corporate sponsors: Millipore(Jim Henderson) Carl Zeiss Microscopy LLC (Sam Byerly) Molecular Dimensions (Issa Isaac) Qiagen (Andrew Fritts) Rigaku (Angela Criswell) TTP Labtech (Melanie Adams) Anatrace (Ed Pryor) Hinds Instruments (Connie Wimmer) Beckman Coulter (Jona Kristo) Mitegen (Ben Apker) Fisher Scientific (Keven Peterson) Sigma Aldrich (Rick Belcher)

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phenix.AmberPrep
by Liu, Jing-Yuan 01 Apr '16

01 Apr '16

Dear PHENIX Developers, I would like to perform phenix.refine using amber gradient. I installed AmberTools 15 and the newest version of Phenix by following the instruction found here http://www.phenix-online.org/documentation/reference/amber.html.<http://www.phenix-online.org/documentation/reference/amber.html> However, when I ran"phenix.AmberPrep", it complains "phenix.AmberPrep not found". In dead, I cannot find any binary named "phenix.AmberPrep". However, it looks to me that phenix is installed OK and so does AmberTools 15. I checked each step of my installation, I could not find anywhere is wrong. Can you please help me out? Thank you! Sincerely, Jing-Yuan

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