- phenixbb - phenix-online.org

R: problem refining RNA structure at 4Å resolution
by fulvio.saccoccia＠uniroma1.it 29 May '13

29 May '13

Any signs of twinning? Check also the correctness of your space group: probably you could index In a lower symmetry Laue group with a slight increased distorsion index. Fulvio ----Messaggio Originale---- Da: Benoît Masquida Inviato: 29/05/2013, 14:53 A: PHENIX user mailing list Oggetto: [phenixbb] problem refining RNA structure at 4Å resolution Dear phenix users, I solved using MR a low resolution RNA structure taking data up to 4.3Å and a model of a structure with slight differences. However, when I try to refine, Rwork decreases quickly (start 47, final 32 but Rfree remains high (start 48, final 44). The data are pretty good up to 4.0 with I/sigma above 1. The map doesn't point clearly to wrong regions of the model. What can I try to improve the maps and build the correct model? Thanks in advance. Benoit _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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problem refining RNA structure at 4Å resolution
by Benoît Masquida 29 May '13

29 May '13

Dear phenix users, I solved using MR a low resolution RNA structure taking data up to 4.3Å and a model of a structure with slight differences. However, when I try to refine, Rwork decreases quickly (start 47, final 32 but Rfree remains high (start 48, final 44). The data are pretty good up to 4.0 with I/sigma above 1. The map doesn't point clearly to wrong regions of the model. What can I try to improve the maps and build the correct model? Thanks in advance. Benoit

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Re: [phenixbb] paired refinement in phenix gui
by Kay Diederichs 28 May '13

28 May '13

On Mon, May 27, 2013 at 15:08:26 -0700, Nat Echols wrote: >> >It would be nice if you could confirm if my settings are ok, or if there are >> >still some settings in the background which I overlooked, because we see >> >small changes in R and Rfree. > Changes relative to what? It is not expected that feeding the output > PDB file back to phenix.refine (or another program) will exactly > reproduce the R-factors from the previous round of refinement, because > the precision of the atomic parameters is limited by PDB format. > (Using mmCIF instead would be more reliable, but we don't think a > change in R-factor of 0.0004 is worth worrying about anyway.) > >> >I added the model refined at higher resolution (e.g. 1.5A) and the mtz file >> >cut at CC (e.g.1.5A) in the ?Input data? tab, and set High resolution cutoff >> >in ?X-ray data and experimental phases? box to (e.g. 1.8A) >> >In the refinement setting strategy tab I uncheck everything and set Number >> >of cycles = 1. >> >In ?other options? I uncheck everything too. > This sounds correct, but it's much easier to simply run the validation > GUI, because the underlying code (specifically phenix.model_vs_data) > is designed to calculate identical R-factors to what phenix.refine > shows you. From what I've seen, recent phenix.model_vs_data works correctly and reproduces the statistics from phenix.refine within the numerical accuracy that one can expect. > >> >Alternatively adding a file to the input data with > I don't recommend this - using parameter files as input is fine for > large repetitive parameter blocks such as custom geometry restraints, > selections from the TLSMD server, or nucleic acid base pairs, but > anything that attempts to override the controls in the main GUI may > not work. > >> >2. For whatever reason I would like to do that (molprobity) - can I (and how >> >can I do this) add the command line commands also in the gui? > Could you please clarify? > >> >3. In december 2012 there was a discussion about weak data and refinement. I >> >would like to know if there are new data available showing that ?Whether the >> >benefit they describe is considered cosmetic or non-trivial,.....? > Maybe Kay could comment on this... There is not a single answer that fits all situations. When done correctly (e.g. keeping Rfree flags, keeping refinement strategy), in those cases that I looked at, using weak reflections (cutoff at <I/sigma>~0.5 to 1, cc1/2~0.15-0.25) improved the model's Rfree at lower resolution (paired refinement!) by a few percent, compared to cutting the data at I/sigma>2. Just try it and see if the improvement is worth it, according to your own judgement! > >> >4. Additionally could one short comment on what phenix is doing with strong >> >(weak) reflections marked as aliens in XDS. > Assuming that XDS doesn't actually remove these, phenix.refine may or > may not discard them at the outlier filtering stage (which can be > disabled). I don't know how the different methods for flagging > suspect resolutions compare; Kay and/or Pavel would know more about > this. The "Alien" list in CORRECT.LP was only (originally) meant to alert the user to ice reflections, zingers, and cosmic rays (not sure if the latter play a role, but the former certainly do!). If the "Alien" list just shows reflections at very high resolution, in low-<intensity> resolution shells, then this is due to the fact that Wilson statistics does not hold in these shells, and therefore the algorithm for deciding about "Aliens" is no longer valid. If this happens, you should (as identified in analysis together with James Holton) prevent CORRECT from marking "Aliens" as outliers by changing REJECT_ALIEN from 20 (the default) to 100 or so. Otherwise the mean intensity in that resolution shell will drop (due to rejecting the strongest reflections), and that is bad for applying the Wilson&French algorithm. The XDSCONV in the latest XDS package (identifying itself as March-30-2013) has two fixes for dealing with weak data (again, based on an exchange with James Holton). Unfortunately, a small bug (affecting very few datasets) was identified by Graeme Winter (thanks!) in the XDS program of that package, so be prepared to download the XDS package again in a few days. hope that helps, Kay > >> >According to the supplementary of P. Andrew Karplus, Kay Diederichs ?Linking >> >Crystallographic Model and Data Quality? >> >I would like to do >> >anisotropic refinement, with additional options >> >?ordered_solvent.new_solvent=anisotropic >> >adp.individual.anisotropic="not element H" >> >fix_rotamers=True?. > If your resolution really is 1.5?, I wouldn't recommend making waters > anisotropic. There is some difference of opinion whether anisotropic > refinement of protein atoms is acceptable; it's probably good to try > both ways. (It would be interesting to know whether including the > weak high-resolution data allows you to parameterize the model more > aggressively.) > > -Nat > -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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PDB deposition
by Kay Diederichs 27 May '13

27 May '13

Dear Phenix developers, the following questions came up today, during an attempt to answer the questions that the PDB asks at deposition time: a) For Bulk solvent modeling, what should be given as value for K sol and B sol ? My understanding is that the new solvent model does no longer result in these values; the table is Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work <Fobs> <Fmodel> kiso kani kmask 37.014-13.525 85.34 95 4 7.2146 38.755 318.867 0.937 1.000 0.300 13.240-10.663 91.82 91 10 7.1453 40.328 328.027 0.901 1.000 0.309 10.640-8.570 93.27 202 6 7.4011 38.069 318.901 0.905 1.002 0.310 8.548-6.875 95.70 380 21 7.2679 31.166 258.647 0.901 1.000 0.309 6.871-5.523 95.40 731 36 7.1964 29.485 241.669 0.908 1.001 0.302 5.520-4.439 90.49 1347 61 7.3445 39.504 329.514 0.934 1.001 0.281 4.438-3.568 92.52 2610 150 7.3166 41.793 347.063 0.961 1.000 0.280 3.567-2.867 94.10 5191 231 7.2983 33.593 278.704 0.965 1.000 0.024 2.867-2.304 92.97 9835 476 7.3098 23.922 198.755 0.984 1.000 0.000 2.304-1.852 92.81 18869 947 7.3097 18.746 155.751 1.053 1.000 0.000 1.852-1.488 90.33 35341 1797 7.3288 10.914 90.931 1.035 0.999 0.000 1.488-1.196 86.49 64979 3561 7.2975 6.848 56.810 1.028 0.998 0.000 1.196-1.081 53.28 29672 1567 7.1776 5.351 43.737 0.986 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0072 So what can we do here? b) there is the question about Overall Anisotropic values B11; B22; B33; B12; B13; B23.... but the logfile offers overall anisotropic scale matrix: V0: -0.0214,0.0415,-0.0249,0.0006,-0.0515,-0.0161 V1: -0.0055,-0.0022,0.0080,-0.0001,-0.0020,0.0011 So which of these should be given? I've tried to locate the information about these two questions in the documentation, but it seems I missed it! thanks, Kay

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command line molprobity tools
by Engin Özkan 27 May '13

27 May '13

Hi everybody, I want to create a comprehensive, human-readable log file by running validation using molprobity tools within phenix command-line. I do not have structure factors/maps. Apparently, the GUI runs validation through phenix.model_vs_data (according to the .eff file), but in command-line, I cannot get phenix.model_vs_data to run without an mtz/hkl. I guess I could provide it a fake data file, and then set the comprehensive flag to "True"? BTW, the log file produced by the GUI is not comprehensive at all. I could not find a related mmtbx or cctbx function either. Another mentioned tool, phenix.validate, does not even exist in my installation (dev 1361). Thanks, Engin -- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 w ph: (650)-498-7111 cell: (650)-862-8563

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Fwd: [ccp4bb] "Formageddon" is upon us... Important news from wwPDB!
by Paul Adams 24 May '13

24 May '13

Begin forwarded message: > From: Gerard DVD Kleywegt <gerard(a)XRAY.BMC.UU.SE> > Subject: [ccp4bb] "Formageddon" is upon us... Important news from wwPDB! > Date: May 24, 2013 11:20:51 AM PDT > To: CCP4BB(a)JISCMAIL.AC.UK > Reply-To: info(a)wwpdb.org > > Dear colleagues, > > I would like to draw your attention to a notification from the wwPDB partners about "Deposition and Release of PDB Entries Containing Large Structures" - see: > > http://www.wwpdb.org/news/news_2013.html#22-May-2013 > > There are major changes afoot in the way large structures are handled in the PDB, as well as in the deposition and annotation procedures and software used by the wwPDB sites. This is of immediate relevance for depositors and users of large structures, but also for software developers and anyone who routinely processes the entire PDB archive or its weekly releases (bioinformatics resources, etc.). From 2014, it will affect essentially everyone who deposits, uses or processes PDB entries. > > If you have any questions about the new deposition system or the procedures for handling large structures or any of the other changes, please contact: info(a)wwpdb.org > > Please pass on this information to anyone likely to be affected by the upcoming changes. Thanks! > > > On behalf of the Worldwide Protein Data Bank, > > --Gerard Kleywegt > > --- > Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK > gerard(a)ebi.ac.uk ..................... pdbe.org > Secretary: Pauline Haslam pdbe_admin(a)ebi.ac.uk -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Invitation to Participate in a NSF-funded workshop/conference
by Sibo Jiang 24 May '13

24 May '13

Invitation to Participate in a NSF-funded workshop/conference Dear Colleagues in Structural Biology, Recently we have received a NSF grant helping to build the community networks and find solutions for the challenging problems. We have also discussed with the program officer of US National Science Foundation on planning for a research conference/workshop series proposal to US NSF. This conference/workshop series will particularly focus on the technical issues and practical challenges in structural biology of nucleic acids, protein-nucleic acid complexes and small molecule-nucleic acid complexes. These challenges include crystallization, derivatization, phasing and high-resolution structure determination. You are invited to participate in this conference/workshop series. If you are interested in our invitation, please reply this email or send your email to huang(a)gsu.edu<mailto:[email protected]>. In your email, please let us know your name, research interests (up to five key words), affiliation and phone number. The details will be announced later. Colleagues in academia are encouraged to forward this email to your friends and colleagues in industry. Colleagues in industry are particularly welcome. Sincerely, The Planning Committee of the NSF-funded Conference/Workshop

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FW: need suggestion
by afshan490＠yahoo.com 24 May '13

24 May '13

<br/><br/><br/>Sent from Yahoo! Mail for iPhone

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From Dmitri Svergun and Matthias Wilmanns: 11th International Conference: Biology and Synchrotron Radiation (BSR)
by Terwilliger, Thomas C 24 May '13

24 May '13

11th International Conference: Biology and Synchrotron Radiation (BSR) 8-11 September 2013, EMBL Hamburg, Germany Abstract submission deadline is approaching – 1st June 2013! Join us in Hamburg, Germany for BSR 2013! Scientists at all possible career levels are invited to this meeting. Check out our preliminary programme to learn more! http://www.bsr2013.org/BSR13-01/programme/index.html Young researchers are highly welcome to apply for a travel grant from the International Union of Crystallography when registering. http://www.bsr2013.org/BSR13-01/info/index.html Present your work! Selected talks and poster sessions provide great opportunities for participants to present their work. Unique networking opportunities are also available to meet colleagues, friends and future collaboration partners from all over the world. Discover the city of Hamburg! BSR 2013 includes a social programme with boat trips and day and night excursions. Accompanying persons will enjoy special rates! http://www.bsr2013.org/BSR13-01/attractions/index.html A tour of DESY’s most impressive research infrastructures - including PETRA, FLASH and the future X-FEL – is included in the registration fee. http://www.bsr2013.org/BSR13-01/desy/index.html Dates at a glance: · Registration and abstract submission: 1 June 2013 · Registration without abstract: 1 August 2013 Take a look at the updated BSR webpage (www.bsr2013.org<http://www.bsr2013.org>) for more information and to register. CONTACT Diah.Yulianti(a)embl.de<mailto:[email protected]> Alternatively, contact us on the event facebook page https://www.facebook.com/events/332259356868854/

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Call for Proposals: IMAGINE, a New Neutron Crystallography Diffractometer
by Meilleur, Flora 23 May '13

23 May '13

IMAGINE, Neutron Crystallography Diffractometer High Flux Isotope Reactor (HFIR), Oak Ridge National Laboratory Call for proposals for experiments anticipated to run from August through December 2013 You are invited to apply for beam time on the neutron quasi-Laue diffractometer IMAGINE, at the High Flux Isotope Reactor. Proposal will be accepted via the web-based proposal system until NOON Wednesday, July 31, 2013. This call is for experiments anticipated to run from August through December 2013. Please see the attached flyer for additional information. For technical information about the capabilities of IMAGINE go to neutrons.ornl.gov/imagine/<http://neutrons.ornl.gov/imagine/> or contact Flora Meilleur, meilleurf(a)ornl.gov, or Andrey Kovalevsky, kovalevskyay(a)ornl.gov. Flora Meilleur, Ph. D Assistant Professor, Molecular and Structural Biochemistry North Carolina State University IMAGINE lead scientist, Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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conflicting bond_simple restraints
by Jianxun Qi 23 May '13

23 May '13

Hi, I had a phosphoserine (SEP) in my structure that is attached in this message. The data_link file for SEP already exists in the mon_lib (data_link_SEPC-N) and the corresponding cif_link I used is as follow: refinement.pdb_interpretation { apply_cif_link { data_link = "SEPC-N" residue_selection_1 = "chain C and resname PHE and resid 3" residue_selection_2 = "chain C and resname SEP and resid 4" } apply_cif_link { data_link = "SEPC-N" residue_selection_1 = "chain C and resname SEP and resid 4" residue_selection_2 = "chain C and resname ARG and resid 5" } } When I run the phenix.refine (my version is phenix-1.8-1069), it said conflicting bond_simple restraints: Sorry: Conflicting bond_simple restraints: 1. definition from: residues: PHE + SEP 2. definition from: residues: PHE + SEP atoms: "ATOM 3121 C PHE C 3 .*. C " "ATOM 3192 N SEP C 4 .*. N " Has anyone ever experienced this case before? Any hints are welcome. Regards Jianxun Qi May 22,2013

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Ca occupancy in multiple soaked structures
by Daniel Slade 22 May '13

22 May '13

Hi Everyone, I have a complex case of data analysis I would love some opinions on. I have a group of structures of a protein that binds 6 calciums, and we want to know the order/concentration at which they fill. The crystals were soaked with calcium from 0-10 mM and all are 1.6-2.1 A in resolution. I determine the order of the calcium binding, and now I am working on the percent occupancy at each concentration. To do this, I have removed the calciums, and then performed simulated annealing for each structure from 2.1-30A resolution to 'normalize' them. I then look at the omit map and scroll out to find the peak sigma intensity of where the calciums should be. The curves fit very well for each calcium, and the numbers correspond well with other solution studies we have. My thought is that I need to normalize this in another way, so I thought choosing a water molecule that is present in all of the structures and removing it, then performing simulated annealing would be a good idea to normalize the peak intensity for each calcium soak concentration, since this water molecule shouldn't change occupancy. Is this the proper way to do this, or can you guys suggest a better way to go about this. I also looked at B factor and e/A3, but that isn't as consistent as peak sigma. Thanks in advance. Dan Daniel J. Slade, Ph.D. Research Associate Thompson Lab The Scripps Research Institute 130 Scripps Way Jupiter, FL 33458 (561) 228-3213

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43rd Mid-Atlantic Macromolecular Crystallography Meeting -- reminder
by Charles Pemble 22 May '13

22 May '13

*43**rd** Mid-Atlantic Macromolecular Crystallography Meeting* *May 30 – June 1, 2013* *Duke University* *Durham, NC* This is a reminder for the 43rd Mid-Atlantic Macromolecular Crystallography Meeting, which will be held next week, May 30-June 01 at Duke University in Durham, North Carolina. Registration and details can be found at http://www.mid-atlantic.org. We encourage you to submit your abstracts for a poster presentation as the deadline is fast approaching! *DEADLINES (updated):* Abstract submission for poster - Next Monday, May 27th *No deadline for registration With best wishes on behalf of the primary Organizing Committee, Charlie Pemble _____________________________ Charles W. Pemble IV, Ph.D. Duke University Medical Center 308 Research Drive LSRC, A06 Durham, NC 27708 charles.pemble(a)duke.edu We thank our current sponsors for their generous contributions: Rigaku Americas Corporation, Agilent Technologies Inc., GlaxoSmithKline, Art Robbins, Bruker, HKL Research Inc., Molecular Dimensions, Hampton Research, Labcyte, GenScript, Genentech, Emerald BioSystems, TTP LabTech, Oxford Cryosystems, PhD Posters, Duke University School of Medicine, Duke Human Vaccine Institute, and Avanti Polar Lipids Inc.

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Workshop - The Future of Microfocus Protein Crystallography - 24-25 September, 2013, Lund, Sweden
by Marjolein Thunnissen 22 May '13

22 May '13

Dear all, I would like to announce a workshop on "The Future of Microfocus Protein Crystallography" which will take place at the MAX IV User meeting on the 24th and the 25th of September, 2013, in Lund, Sweden. Recent developments within protein crystallography methods in combination with the possibilities offered by the new upcoming synchrotron sources such as the MAX IV 3 GeV storage ring make possible exciting new ways of carrying out research within structural biology. Small microfocus beamlines with a very high flux and increased coherence will make new types of experimentation possible. The scientific possibilities will be highlighted through a series of talks by experts showing the impact of the new type of X-ray sources and microfocus beamlines on research within structural biology. The new generation of microfocus beamlines will also set a high demand on instrumentation and suitable software. For example, data collection will potentially be very fast (in milliseconds) and radiation damage will allow only a limited amount of data to be collected from each sample. New technical solutions for sample handling and presentation, data processing methods and more will be needed for these types of experiments, and these will also be presented and discussed at the workshop. Confirmed speakers include David Stuart, Daniel Wacker, Simone Weynand, Jens Preben Morth, Tove Sjögren, Richard Neutze, Janet Smith, Alke Meentz, Alexei Soares, Thomas White and Clemens Schulze-Briese The workshop is part of a process to obtain an updated proposal for the possible Phase 2b beam line MicroMAX at the upcoming new 3 GeV storage ring of MAX IV in Lund. This workshop should give the user community an opportunity to explore the scientific possibilities of a new generation of microfocus beam lines, but also it will give them the chance to contribute with specific input on their own experimental demands on the beam line. The workshop is part of the MAX IV laboratory user meeting. Registration will be through the user meeting website which will open for registration soon. Further information on this workshop can be found at https://www.maxlab.lu.se/node/1609 and for the MAX IV user meeting at https://www.maxlab.lu.se/um13 . For the organisers, Richard Neutze, Gunter Schneider and Gregers Rom Andersen Marjolein Thunnissen ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)76-632 0417 Associate Professor Fax +46-(0)46-22 24692 Dept of Biochemistry and Structural Biology, Lund University http://www.mps.lu.se<http://www.mps.lu.se/> PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator MX (The MAX IV Laboratory): I911 and BioMAX ________________________________________________________________________

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depositing pdb files
by Mengbin Chen 21 May '13

21 May '13

Hi Phenix Users, I am going to deposit some pdb files into RCSB, which requires Luzzati plots and a bunch of other things. I don't know how to get these results from Phenix (actually the main problem is luzzati errors, Phenix does not seem to provide them), although SFcheck from CCP4i provides only some of them. I know CNS can do this by model_stats.inp, but that's too much trouble since I have complicated ligands bound. Any suggestions would be appreciated! Thank you in advance, Mengbin -- Mengbin Chen Department of Chemistry University of Pennsylvania

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mr_rosetta: how to continue from recovered mr_protocols.default run
by Christian Becke 21 May '13

21 May '13

Hi, I am trying mr_rosetta on a complex. At the GROUP_OF_ROSETTA_REBUILD stage, my machine ran out of memory and the mr_protocols.default processes were killed. After adding more swap space, I restarted the mr_protocols.default runs (3 parallel jobs, one for each chain) using the scripts RUN_?/WORK_?/run_rebuild.sh, which appear to have finished correctly (i.e., there are 20 pdb files generated for each of the chains). However, I could not figure out how to restart mr_rosetta so that it picks up these models. Any suggestions? Thanks, Christian

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Grid size in max_entropy maps
by Schubert, Carsten [JRDUS] 20 May '13

20 May '13

Is there a way to control the grid size in the maximum entropy maps? The current grid size is quite small, resulting in a very fine mesh. Thanks Carsten

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43rd Mid-Atlantic Macromolecular Crystallography Meeting
by Charles Pemble 10 May '13

10 May '13

*43**rd** Mid-Atlantic Macromolecular Crystallography Meeting* *May 30 – June 1, 2013* *Duke University* *Durham, NC* *ANNOUNCEMENT: *We have extended the deadline for submitting abstracts to be considered for presentations until midnight Sunday, May 12. Registration and details can be found at http://www.mid-atlantic.org. The 43rd Mid-Atlantic Macromolecular Crystallography Meeting, will be held at Duke University in Durham, North Carolina. This year will feature keynote speaker Tom Terwilliger from Los Alamos National Lab, workshops on PHENIX and MolProbity, plus many talks & posters on new and exciting research. The best presentation and poster by a Graduate Student & Postdoctoral Fellow will be awarded (total of 4). We encourage you to submit your abstracts and sign up for the workshops as these are separate processes from registration. *DEADLINES (updated):* Abstract submission for presentation - May 12th Abstract submission for poster - May 27th *No deadline for registration With best wishes on behalf of the primary Organizing Committee, Charlie Pemble _____________________________ Charles W. Pemble IV, Ph.D. Duke University Medical Center 308 Research Drive LSRC, A06 Durham, NC 27708 charles.pemble(a)duke.edu We thank our current sponsors for their generous contributions: Rigaku Americas Corporation, Agilent Technologies Inc., GlaxoSmithKline, Art Robbins, Bruker, HKL Research Inc., Molecular Dimensions, Hampton Research, Labcyte, GenScript, Genentech, Emerald BioSystems, TTP LabTech, Oxford Cryosystems, PhD Posters, Duke University School of Medicine, Duke Human Vaccine Institute, and Avanti Polar Lipids Inc.

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Submissions for next CCN newsletter
by Nigel Moriarty 07 May '13

07 May '13

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the June 2013 issue is 31 May, 2013 but if you can send me drafts before the 15th of May we can get started on generating proofs. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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43rd Mid-Atlantic Macromolecular Crystallography Meeting
by Charles Pemble 07 May '13

07 May '13

*43**rd** Mid-Atlantic Macromolecular Crystallography Meeting* *May 30 – June 1, 2013* *Duke University* *Durham, NC* This is a reminder for the 43rd Mid-Atlantic Macromolecular Crystallography Meeting, which will be held at Duke University in Durham, North Carolina. This meeting fosters discussion and interaction among structural biologists from around the Mid-Atlantic region. Registration and details can be found at http://www.mid-atlantic.org. The deadline for registration is May 15th. This year will feature keynote speaker Tom Terwilliger from Los Alamos National Lab, workshops on PHENIX and MolProbity, plus many talks & posters on new and exciting research. Presentations will be selected from submitted abstracts and preference will be given to young researchers. The best presentation and poster by a Graduate Student & Postdoctoral Fellow will be awarded (total of 4). We encourage you to submit your abstracts and sign up for the workshops as these are separate processes from registration. *DEADLINES:* Registration - May 15th Abstract submission for presentation - May 10th Abstract submission for poster - May 27th *IMPORTANT: *A block of rooms have been reserved at the Millennium hotel as well as the Duke dormitories. The deadline for reserving a room at the Millennium is May 9th. With best wishes on behalf of the primary Organizing Committee, Charlie Pemble _____________________________ Charles W. Pemble IV, Ph.D. Duke University Medical Center 308 Research Drive LSRC, A06 Durham, NC 27708 charles.pemble(a)duke.edu We thank our current sponsors for their generous contributions: Rigaku Americas Corporation, Agilent Technologies Inc., GlaxoSmithKline, Art Robbins, Bruker, HKL Research Inc., Molecular Dimensions, Hampton Research, Labcyte, GenScript, Genentech, Emerald BioSystems, TTP LabTech, Oxford Cryosystems, PhD Posters, Duke University School of Medicine, Duke Human Vaccine Institute, and Avanti Polar Lipids Inc.

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Morphing only a part of the model?
by Guenter Fritz 06 May '13

06 May '13

Dear all, I am working on a multisubunit protein complex (ca. 2000 residues). I would like to morph only a part or one subunit into the experimental electron density without morphing the rest of the protein. iIs there a way to select a subunit or a part of the model? Best regards, Guenter

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Find Difference peaks and holes
by John Rose 03 May '13

03 May '13

Hi, I can't seem to find the "Find Difference peaks and holes" utility in the PHENIX 1.8.2-1309 distribution. I found it to be very useful. Can you tell me where it is hiding. Regards, John John Rose Ph.D. Associate Professor B204B, The Fred C. Davison Life Sciences Complex 120 Green Street Department of Biochemistry and Molecular Biology University of Georgia Athens, GA 30602-7229 ========================================= Phone: 706-542-1750 Fax: 706-542-3077

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ReadySet & phenix.refine problem: NAG-Asn with hydrogen atoms
by Zhijie Li 29 Apr '13

29 Apr '13

Hello, I am refining my structure with hydrogen atoms on (phenix 1.8.2-1309). The protein contains two Asn-linked GlcNAc. I noticed two problems with respect to the NAG-Asn linkage in the presence of hydrogen atoms: 1) After running ReadySet (to add hydrogen to the PDB ab initio), the H1 on the NAG is pointing to the amino group of Asn, ie, the NAG seems to be interpreted as in its alpha anomer instead of beta (should be GlcNAc beta1,N-Asn). This is not really a problem as it doesn't seem to affect the refinement. 2) The H21 in Asn is correctly removed by ReadySet, leaving only H22. However, if I send this PDB to phenix.refine, the refinement will fail almost instantly complaining that H22 of the Asn has an unknown nonbonded energy type symbol. But if I simply change the atom name of H22 to H21, the refinement will proceed to completion with no problem, only leaving an H21 at the position where H22 should be. I was not sure what caused this error. So I trimmed my PDBs down to the Asn and NAG only, and fed the small PDB to ReadySet and phenix.refine (with an eff file indicating the NAG-Asn linkage) and got the same behavior: H22 on Asn - error; H21 on Asn - OK. I hope someone can look into this. Thanks in advance. Zhijie

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SIGF in refinement
by Aksyuk, Anastasia (NIH/NIAMS) [F] 29 Apr '13

29 Apr '13

Hi, I was wondering how SigFobs values are used in phenix refinement and how important those are. I am asking in view of P1 space group with low redundancy or even cryo-EM map based Fobs. Maybe you can point me to a useful reference on likelihood targets. I feel lost in those that I have. Thanks, --Anastasia ------------------------------ Anastasia A Aksyuk, PhD Laboratory of Structural Biology, NIAMS Bldg 50, Room 1511, 50 South Drive MSC 8025 N.I.H., Bethesda, MD 20892-8025 tel 301 451-8247 e-mail: anastasia.aksyuk(a)nih.gov

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Re: [phenixbb] clashscore discrepancies
by Alex Theodossis 27 Apr '13

27 Apr '13

Dear phenixbb, I have carried out refinement using the latest version of PHENIX, which gives improved molprobity stats. However, these stats still do not match those porvided by the molprobity server: PHENIX output Molprobity server Existing H-model Electron-cloud H-model All atom clashscore 2.57 4.2 (81st perc) 3.25 (88th percentile) Rotamer outliers 0.7 1.14 1.14 Overall score 1.04 1/24 (89th perc) 1.16 (93rd percentile) Given that PHENIX is now giving me the best results and all scenarios give reasonable results I am less inclined to be concerned. However, I still find these inconsistencies rather puzzling and am curious to learn what is causing them. Thanks in advance.

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