- phenixbb - phenix-online.org

Re: [phenixbb] Real space refinement
by Pavel Afonine 18 Feb '14

18 Feb '14

Hi Mavis, there are two options. One is convert your EM map into structure factors Fobs and HL coefficients using phenix.map_to_structure_factors command and then use phenix.refine to do reciprocal space refinement. This is somewhat indirect way. The good thing about it is that phenix.refine has a broad range of tools to handle low resolution refinement. Another option is to use phenix.real_space_refine to refine model against the map directly. This is a preferred way but phenix.real_space_refine is new, less mature program and it generally is still under development (though it's functional if you try it now). So if it does not work as you expected or you have any feature requests or any questions or any other feedback - please do not hesitate to let me know, as this may help to improve this tool. All the best, Pavel On 2/17/14, 6:14 AM, Agbandje-Mckenna,Mavis wrote: > Dear Pavel, > > Thank you so much for getting back to me - this is much appreciated. We received a script from Hong Zhou's group who have been using Phenix to refine the model for their 3.3 Angs cryo-EM Aquareovirus structure that we were going to try but this seems a lot more simpler! > > Thanks again. I will let you know how it turns out. > > And thank you for the attached pdf. > > Best wishes > > Mavis > > Mavis Agbandje-McKenna, Ph.D. > Director, Center for Structural Biology > Professor, Dept. of Biochemistry and Molecular Biology > Center for Structural Biology > The McKnight Brain Institute > P.O. Box 100245 Tel.: 1-352-392-5694 > University of Florida Fax.: 1-352-392-3422 > Gainesville, FL 32610-0245 e-mail: mckenna(a)ufl.edu > Website: http://msg.mbi.ufl.edu > ________________________________________ > From: Pavel Afonine [pafonine(a)lbl.gov] > Sent: Monday, February 17, 2014 2:28 AM > To: Agbandje-Mckenna,Mavis; phenixbb(a)phenix-online.org > Cc: Lins, Bridget; Drouin,Lauren M > Subject: Re: Real space refinement > > Hi Mavis, > > you can do it in Phenix. Command line tool for this is: > phenix.real_space_refine. Just give it map and model and see what > happens, like this: > > phenix.real_space_refine model.pdb ccp4_formatted_map.map > > I wrote this program specifically to do various kinds of model > refinement against the map, with the main focus on EM maps. Have a look > at the article that briefly describes it here: > http://www.phenix-online.org/newsletter/CCN_2013_07.pdf > "New tool: phenix.real_space_refine". > The article is from last year but I haven't done much since then so it > pretty much documents the current state of the art. > > Should you have any questions or problems or need any help with this > please let me know off list. > > All the best, > Pavel > > On 2/14/14, 8:45 AM, Agbandje-Mckenna,Mavis wrote: >> Dear Pavel, >> >> I don't believe we have met, but you have received several e-mails from people in my group (including Sujata (Tina) Halder) and also helped them with their use of Phenix - thank you. >> >> I have a question for you regarding real space refinement in Phenix. We have a 3.7 Angs cryo-EM reconstructed structure for a virus capsid and we have been able to build a model for the capsid VP using COOT. I would like to refine this model further against the map using real space refinement. I am trying to find a suitable program that would allow me to do this. I believe Phenix can do it, but I am not sure. Could you give me some direction? >> >> Thanks in advance. >> >> Best wishes >> >> Mavis >> >> Mavis Agbandje-McKenna, Ph.D. >> Director, Center for Structural Biology >> Professor, Dept. of Biochemistry and Molecular Biology >> Center for Structural Biology >> The McKnight Brain Institute >> P.O. Box 100245 Tel.: 1-352-392-5694 >> University of Florida Fax.: 1-352-392-3422 >> Gainesville, FL 32610-0245 e-mail: mckenna(a)ufl.edu >> Website: http://msg.mbi.ufl.edu

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Gordon Conference on Diffraction Methods in Structural Biology
by Anastassis Perrakis 17 Feb '14

17 Feb '14

Dear all, The biannual Gordon Research Conference in Structural Biology, accompanied by the first Gordon Research Seminar, will take place in the last week of July at Bates College, New England, a few hours drive from the IUCr meeting that follows in the first week of August. The theme for the GRC is "Faster, Smaller, Better: Novel Technologies for Diffraction Experiments in Molecular Biology and Drug Discovery" and of the GRS (which precedes the GRC and is targeting young scientists giving them an opportunity to present their own work to their peers prior to the meeting) "Towards Integrative Structural Biology". We have a truly fantastic line of speakers and discussion leaders, including John Kuriyan , Randy Read, Ana Gonzales, Ilme Schlichting , Henry Chapman , John Spence, Graeme Winter , Aina Cohen, Thomas Schneider , Gwyndaf Evans , Bob Fischetti , Flora Meilleur, Janet Newman , John Hunt , Michael Duszenko , Jose Antonio Marquez, Paul Adams , Clemens Vonrhein , Airlie McCoy , Brent Nannenga, Zbyszek Dauter , Tom Terwilliger , Garib Murshudov , Gerard Kleywegt , Paul Emsley, Dmitri Svergun , Peter Zwart , Michael Hammel , Lois Pollack, Elspeth Garman, Lisa Keefe , Gary Gililland , Aydnan Achour and Giovanna Scapin. For more details visit our web site: https://www.grc.org/programs.aspx?year=2014&program=diffrac And here is the largely unavoidable motivational speech for anyone interested to my highly biased personal view: I first went to this meeting in 1998, as a young post-doc, presenting results that later led to the 'ARP/wARP' software: in fact, I had changed my slides (for the younger audience: slides were pieces of photographic film that were typically projected as mirror images of what you really wanted) a month or so before the meeting, as we got our very first models auto-built. I thought it was the most educational and exciting meeting I have ever been to, and in many ways it has shaped my research plan and my career (and my hate for golf). I wish I could also say that I never missed any of the subsequent meetings, but courtesy of the US Visa authorities and the Greek Army, I actually did a miss a couple. However, I still find them as exciting as so many years ago, but for a whole different set of scientific reasons: the diffraction methods landscape is changing rapidly, new machines and concepts make possible experiments that we do not even know what they are going to be! I am honored to be chairing this year's edition, and I hope that I will hear from at least one of you, what I had heard from a few before: "this is the best meeting I have been in my life". Science aside, I am glad there is no golf course nearby the Bates College site where we are holding this meeting for the last decade, I am equally happy for the "Great Outdoors" site where we do the mid-week excursion, and I am looking forwards to the football (sorry: "soccer") and basketball games. The Bates College boasts an excellent auditorium for the talks, a truly outstanding lounge for the poster sessions (that are always accompanied by drinks, an observation that might partially explain the tendency to finish well after midnight in a very positive spirit) and a somewhat confusingly and an unexpectedly good quality restaurant in the very friendly College site. A limited amount of (partial) bursaries to young scientists will be available for this year - when this becomes definitive we will post the news. I should also mention that one session will host eight seminars that will be selected from the poster sessions, giving all particpants the opportunity to present their own research! In the meantime, I am looking forward to welcome you all at the meeting and I hope you will register ... today! Best regards, Tassos Anastassis (Tassos, Perrakis, Principal Investigator , Staff Member Department of Biochemistry (B8, Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile , SMS: +31 6 28 597791

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Re: [phenixbb] Real space refinement
by Pavel Afonine 17 Feb '14

17 Feb '14

Hi Mavis, you can do it in Phenix. Command line tool for this is: phenix.real_space_refine. Just give it map and model and see what happens, like this: phenix.real_space_refine model.pdb ccp4_formatted_map.map I wrote this program specifically to do various kinds of model refinement against the map, with the main focus on EM maps. Have a look at the article that briefly describes it here: http://www.phenix-online.org/newsletter/CCN_2013_07.pdf "New tool: phenix.real_space_refine". The article is from last year but I haven't done much since then so it pretty much documents the current state of the art. Should you have any questions or problems or need any help with this please let me know off list. All the best, Pavel On 2/14/14, 8:45 AM, Agbandje-Mckenna,Mavis wrote: > Dear Pavel, > > I don't believe we have met, but you have received several e-mails from people in my group (including Sujata (Tina) Halder) and also helped them with their use of Phenix - thank you. > > I have a question for you regarding real space refinement in Phenix. We have a 3.7 Angs cryo-EM reconstructed structure for a virus capsid and we have been able to build a model for the capsid VP using COOT. I would like to refine this model further against the map using real space refinement. I am trying to find a suitable program that would allow me to do this. I believe Phenix can do it, but I am not sure. Could you give me some direction? > > Thanks in advance. > > Best wishes > > Mavis > > Mavis Agbandje-McKenna, Ph.D. > Director, Center for Structural Biology > Professor, Dept. of Biochemistry and Molecular Biology > Center for Structural Biology > The McKnight Brain Institute > P.O. Box 100245 Tel.: 1-352-392-5694 > University of Florida Fax.: 1-352-392-3422 > Gainesville, FL 32610-0245 e-mail: mckenna(a)ufl.edu > Website: http://msg.mbi.ufl.edu

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100 Years of Crystallography
by George Phillips 12 Feb '14

12 Feb '14

Rice University symposium to celebrate 100 years of crystallography HOUSTON – (Feb. 10, 2014) – Rice University and the Gulf Coast Consortia will host an all-day public symposium titled “International Year of Crystallography: Structure Matters” Feb. 14 at the BioScience Research Collaborative. Experts in X-ray crystallography – the technique scientists use to determine the structure of matter at very small scales – will discuss the significance of the technology and how it’s used to visualize the structures of proteins, a critical step in the design of drugs to fight disease. Speakers include George Phillips, the Ralph and Dorothy Looney Professor of Biochemistry and Cell Biology at Rice; Yizhi Jane Tao, an associate professor of biochemistry and cell biology at Rice; Choel Kim, an assistant professor at Baylor College of Medicine; John Spence, the Richard Snell Professor of Physics at Arizona State University and director of science for the National Science Foundation (NSF) BioXFEL Science and Technology Center; and Stephen Burley, professor and director of the Center for Integrative Proteomics Research at Rutgers University. The program will begin at 9 a.m. with poster presentations and science exhibits for high school students. Crystallography is being recognized by the United Nations on the 100th anniversary of the awarding of Nobel Prizes to its discoverers, German physicist Max von Laue and the father-son team of William Henry and William Lawrence Bragg. Rice researchers led by Phillips are part of the NSF’s BioXFEL consortium, founded last year and based at the University of Buffalo, to explore the use of strong X-ray lasers to detail the atomic structures of molecules with a resolution approaching the nanoscale. The symposium is free and sponsored by the Gulf Coast Consortium (GCC) for Protein Crystallography, the Wiess School of Natural Sciences, the NSF BioXFEL Science and Technology Center and the Rigaku Corp. Who: Scientists, students and the public. What: “International Year of Crystallography: Structure Matters.” When: Friday, Feb. 14, from 9 a.m. to 5 p.m. Where: Rice’s BioScience Research Collaborative, 6500 Main St. An agenda and registration information are available at the symposium website, http://gcc.rice.edu/2014_Crystallography_Symposium.aspx - See more at: http://news.rice.edu/2014/02/10/rice-symposium-to-celebrate-100-years-of-cr… George N. Phillips, Jr. Ralph and Dorothy Looney Professor Department of Biochemistry and Cell Biology Rice University, MS140 6100 Main Street Houston, Texas 77005-1892 Office: +1 713.348.6951 http://www.bioc.rice.edu/

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mmCIF output _atom_site.B_iso_or_equiv
by Dan McNamara 12 Feb '14

12 Feb '14

Hi all, I have a structure with 96 chains in the ASU and mmCIF format is required for using the RCSB PDB software tools with two-letter chain IDs. That's all fine, but when I use the argument "output.write_model_cif_file=True" with my refinement run, the B-factors reported in the .cif output are not consistent with those in the .pdb output from phenix.refine. Trying to deposit the mmCIF output with U=0.00008 flags their returned final .PDB copy as 0.00. Is there functionality for having the isotropic B-factor equivalent recorded for mmCIF format output? I have not found a way to parameterize phenix.pdbtools so that the mmCIF output has the B-factor the PDB is looking for, and all the information desired from the phenix.refine mmCIF output. I can use "convert to isotropic" and output as mmCIF, but then the ANISOU information from TLS refinement is not retained. Best, Dan

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Phenix refine selection within distance
by Andrew Waight 11 Feb '14

11 Feb '14

Hello All, I am trying select a subsection of my molecule only to run TLS refinement on. I want to select all residues within a certain distance from a given chain. I am using the selection editor within the Phenix interface and can't seem to figure out if Phenix provides this functionality in the view/pick selection editor. The Phenix.refine manual describes some "smart" selections, but they don't seem to work in the selection box. I have tried many variations of. within(5, chain 'H') To no avail. Is this possible to do in the selection editor? Thanks for your help. Andrew Waight

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2014 workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 11 Feb '14

11 Feb '14

Fifth Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 16 - June 20, 2014 Application deadline: April 18, 2014 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome. However the course organization may not be able to offer travel or accommodation support. The number of participants will be limited to 15. There is no registration fees for all selected participants. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (for graduate students only; 1/2 to 1 page), should be sent electronically to meilleurf(a)ornl.gov<mailto:[email protected]> before April 18, 2014. Detailed information can be found on the course web page: http://neutrons.ornl.gov/conf/gcnb2014/ Flora Meilleur, Ph. D Assistant Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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assign multiple ligand conformations
by Wei Shi 11 Feb '14

11 Feb '14

Hi everyone, I am working with protein-ligand complex structure. For the head group in one of the ligands in the structure, two more positions in addition to the current position look possible according to the blue density in Coot. I am thinking of assigning multiple occupancies/positions to this head group. So, I am wondering what I should do to achieve this. Is the following strategy right? 1. Fit the head group to the density at three different positions separately in Coot and save them separately. 2. Find out the atoms that are different among the three ligand positions and combine the same atoms with different positions and change the occupancy of those atoms to something between 0 to 1. 3. Use Phenix. refine to refine. The occupancy refinement should be automatically on, right? Is this the best way to assign multiple occupancies/positions to the head group? Thank you so much! Also, anything to look after refinement which can tell me whether I am assigning the right multiple conformations to the ligand? Thank you so much! Best, Wei

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metal ions in phenix.ensemble_refinement
by Scott Horowitz 11 Feb '14

11 Feb '14

Hi, I'm trying to use phenix.ensemble_refinement, and my structure has several zinc atoms, both coordinated to amino acids and free imidazoles, and sometimes both. It looks as though it's not really understanding that the zincs really should stay more or less in their coordination spots, and are spending some time in kind of weird spots. I couldn't find anything documented that seems like it will help, unless there's some clever way to use the harmonic restraints for this that I haven't figured out. And while I'm at it, I have another potentially related problem: the rfree of my final ensemble (0.27) is substantially higher than my input structure (0.24). And yes, I had been doing my refinement in phenix, with hydrogens added, and I optimized pTLS. If you're curious, this is a 1.9 A structure. Any help and/or suggestions would be greatly appreciated! Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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exporting results, reduce
by jp d 11 Feb '14

11 Feb '14

hi, we have a large complex at low resolution (7A) and just want to see general conformational changes. Occasionally phenix gets stuck at 'Exporting Results' and top shows 'reduce' running and using lots of RAM . so much RAM that it starts using swap. is there a way to bypass or limit the reduce step. thanks jpd

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ACA2014 Albuquerque
by Peter Zwart 10 Feb '14

10 Feb '14

Dear All, This May 24 to 28, the ACA meeting in Albuquerque will be host to an exciting scientific program. There will be workshops covering (Grazing Incidence) Small Angle Scattering, Joined X-ray/Neutron Crystallographic Refinement and the visualization of diffraction data. The Transactions sessions will celebrate the impressive legacy of the first 100 years of Crystallography.The scientific sessions will feature the latest developments in crystallography and scattering methods and is host to host an impressive list of speakers, such as John Helliwell (Patterson Award),Wayne Hendrickson, Axel Brunger, Richard Neutze and Borden Lacy (Etter Early Career award). We are still accepting the submission of abstracts and we encourage you to do so as quickly as possible: (most of) the session leaders have not finalized their session program yet, so there still is an opportunity to get selected to give a talk. Regards Christine Beavers & Peter Zwart

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Running Phenix on a small cluster
by Mads Beich-Frandsen 10 Feb '14

10 Feb '14

Dear all, We have a small cluster running Ubuntu, using the Condor distribution package. –Does anyone have experience in setting up Phenix to run in such an environment? Thanks in advance, /Mads ******************************** Mads Beich-Frandsen, PhD Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona C/ Baldiri Reixac 10 08028 Barcelona - Spain Tel: +34-9340-37188 | Fax: +34-9340-39960 E-mail: mads.beichfrandsen(a)irbbarcelona.org

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RNA sugar pucker
by Benoît Masquida 08 Feb '14

08 Feb '14

Hello everyone, Does someone know how to define the sugar pucker in eLBOW? I am trying to force a C3' endo conformation for GDP. Thanks for your help. Benoit -- Benoît Masquida Chargé de Recherche CNRS GMGM, UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB, 21, rue René Descartes 67084 Strasbourg b.masquida(a)unistra.fr

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Meeting Announcement: Northwest Crystallography Workshop
by Dale Tronrud 07 Feb '14

07 Feb '14

(Pacific) Northwest Crystallography Workshop http://oregonstate.edu/conferences/event/nwcw2014/ June 20-22, 2014 Registration is now open for this year's edition of the Northwest Crystallography Workshop. It is being hosted at Oregon State University in Corvallis in the heart of the Willamette Valley surrounded by wine country, wildlife refuges, and with both the Cascade Mountains and the Pacific Ocean within easy driving distance. It can be easily accessed from either the Portland or Eugene airports. This biennial meeting has been held at various locations in the Pacific Northwest since 1981. It has always proven to be a great venue to meet other researchers in the region who are interested both in using macromolecular crystallography to solve structures and in developing and enhancing methods. The "workshop" part of the name will be taken seriously. We will have talks and posters with priority for speaking slots given to students and post-docs who focus on methodologies or interesting structure determination stories, and/or how structural observations provide insight into function and biology. There will be a reception on Friday evening. On Saturday there will be talks during the day and a banquet followed by a keynote address in the evening. Talks will continue on Sunday morning with the workshop wrapping-up at noon. A light lunch will be served on Saturday and a boxed lunch will be available on Sunday. Register today and get your abstracts submitted anytime between now and the April 30 abstract deadline. We've tried to keep registration costs low and early registration (through April 30) is $75 for students and $100 for others. Reasonably priced on-campus dormitory housing is available and must be arranged at the time of registration. Special rates at two local hotels have been arranged for those who want to book their own lodgings. We look forward to a great meeting and celebration of the International Year of Crystallography. Dale and Andy Dale E. Tronrud and P. Andrew Karplus Department of Biochemistry & Biophysics 2011 ALS Bldg Oregon State University Corvallis, OR 97331 USA

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how to remove hydrogen from pdb
by Afshan Begum 07 Feb '14

07 Feb '14

Dear Experts, Could you kindly tell me how can i remove hydrogen from my coordinate. Actually i refine my structure with phenix along all hydrogen now its almost done but before submitting the molecule into PDB data bank i want to remove hydrogen from the coordinate which i do not know how to do, suggestion would be appreciated Best Regards AFSHAN =========================================== Dr. Afshan Begum

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weight_selection_criteria
by Mark A Saper 06 Feb '14

06 Feb '14

Can anyone explain what the weight_selection_criteria parameters (see below)? How do they interact with other weights. Are they still used if I set optimize_xyz_weight=TRUE? I'm using dev-1616. target_weights optimize_xyz_weight= False optimize_adp_weight= False wxc_scale= 0.5 wxu_scale= 1.0 wc= 1.0 wu= 1.0 fix_wxc= None fix_wxu= None shake_sites= True shake_adp= 10.0 regularize_ncycles= 50 verbose= 1 wnc_scale= 0.5 wnu_scale= 1.0 rmsd_cutoff_for_gradient_filtering= 3.0 force_optimize_weights= False weight_selection_criteria bonds_rmsd= None angles_rmsd= None r_free_minus_r_work= None r_free_range_width= None mean_diff_b_iso_bonded_fraction= None min_diff_b_iso_bonded= None Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan c/o Biophysics, Chem 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

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phenix version 1.8.4
by Rosario Recacha 06 Feb '14

06 Feb '14

Hello, I installed the last version if phenix in ubuntu and whe I want to run it I receive the next message: ImportError: libjpeg.so.62: cannot open shared object file: No such file or directory I installed older versions in other computers following the same indications, and never I have had problems. Thanks in advance. Kind Regards, Rosario

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phenix.autosol and phenix.hyss now optimized for weak SAD data
by Terwilliger, Thomas C 06 Feb '14

06 Feb '14

Hi Phenix users! You might notice some big differences in HySS and AutoSol in the new 2014 versions of Phenix (starting with current nightly builds and the soon-to-be-released Phenix-1.8.5). The big changes are parallelization, the use of Phaser completion in HySS, iterative Phaser completion using maps and models in AutoSol, and on-the-fly optimization of parameters in AutoSol for cases with weak anomalous signal. Now HySS and AutoSol can solve structures with very weak SAD phase information that previous versions could not solve. More details will be in the Phenix newsletter that will come out shortly! You can see documentation on the new HySS at: http://phenix-online.org/version_docs/dev-1613/hyss.htm#anch8 and on the new AutoSol at: http://phenix-online.org/version_docs/dev-1613/autosol.htm#anch118 --Tom Terwilliger, Randy Read, Gábor Bunkóczi, Nat Echols

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Computational Crystallography Newsletter - Volume 5, Number 1
by Nigel Moriarty 05 Feb '14

05 Feb '14

Dear Colleagues, I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. Articles -------- FEL Detectors and ImageCIF Quantum Mechanics-based Refinement in Phenix/DivCon Short communications -------------------- Short Communications Phenix tools for interpretation of BIOMT and MTRIX records of PDB files Coping with BIG DATA image formats: integration of CBF, NeXus and HDF5 Fitting tips #7 - Getting the Pucker Right in RNA Structures 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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Fwd: CCP4 crystallographic summer school in USA, at APS, June 24-July 2
by Nathaniel Echols 04 Feb '14

04 Feb '14

---------- Forwarded message ---------- From: Nukri Sanishvili <rsanishvili(a)anl.gov> To: <phenixbb(a)phenix-online.org> Date: Mon, 3 Feb 2014 18:12:09 -0600 Subject: CCP4 crystallographic summer school in USA, at APS, June 24-July 2 Dear Colleagues, We are pleased to announce the seventh annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2014/index.php<https://mail.anl.gov/owa/redir.aspx?C=Qww5V7BVpECZd8A2kldFSf7_-DvC9NAIxdFZE…> *Title:*"CCP4 crystallographic school: From data collection to structure refinement and beyond" *Dates*: June 24 to July 2. *Site:* Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA *The school content: *Data collection workshop the first two days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three sections - lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. *Applicants*: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. *Application*: Application deadline is April 11. The application form, the program, contact info and other details can be found at http: http://www.ccp4.ac.uk/schools/APS-2014/index.php<https://mail.anl.gov/owa/redir.aspx?C=Qww5V7BVpECZd8A2kldFSf7_-DvC9NAIxdFZE…> *Fees: *There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers can help make the reservations at economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. We hope to see you at the school, Garib, Ronan and Nukri -- Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667rsanishvili(a)anl.gov

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Re: [phenixbb] autosol error// phaser error
by Terwilliger, Thomas C 03 Feb '14

03 Feb '14

Hi Almudena, Can you possibly say what version of Phenix you are using: phenix.version and then the columns in your mtz file: phenix.mtz.dump my_mtz_that_fails.mtz and the inputs you used for autosol and phaser (you can send the top part of the log files that should have this information). Can you also try this little test for resolve model building (that is where the "cannot read segment library" comes from): phenix_regression.wizards.test_command_line_build test_autobuild_quick That would help for diagnosing the problems. All the best, Tom T Hi everyone, I am facing some troubles with PHASER and with AutoSol (things that did not happen earlier to me). I am working with anomalous data and the first thing I do is to run HySS in order to find the heavy atoms sites. Once this is done I have two options: run PHASER or run AutoSol. Phaser gives the following error message: ERROR setting up data inputs (FATAL RUNTIME) Can not find MTZ column "F_SAD_SAD(+)" Instead Autosol gives the following: ERROR sorry can not read segment library Could anyone help me out here? Thank you very much in advance. Best, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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Ten days left, many seats available: Apply for RapiData 2014, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 31 Jan '14

31 Jan '14

We are offering RapiData 2014, the sixteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 27 April - 2 May 2014: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. In addition to MX there will be opportunity for learning about correlated MX and spectroscopy, and SAXS. You'll find the application materials on the Course Application tab at this site. For the twelfth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 27 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be an additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (no more than 30 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply yourself, or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Photon Sciences and Biosciences Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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Output bulk solvent
by Koji Yonekura 29 Jan '14

29 Jan '14

Dear All, I am wondering if Phenix.refine has an option to output bulk solvent F to the mtz file. Best regards, Koji -- Koji Yonekura, Ph. D. Biostructural Mechanism Laboratory RIKEN SPring-8 Center Harima Institute 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan Tel: +81-791-58-2837 Fax: +81-791-58-1844 PHS: +81-791-58-0803 (7803) E-mail: yone(a)spring8.or.jp http://www.riken.jp/biostrmech/

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Postdoctoral position in macromolecular crystallography, HZI Braunschweig, Germany
by Wulf Blankenfeldt 27 Jan '14

27 Jan '14

Postdoctoral Position in Macromolecular Crystallography The Helmholtz Centre for Infection Research (HZI) in Braunschweig (Germany) announces an opening for a postdoctoral researcher in macromolecular crystallography. The position is associated with the department “Structure and Function of Proteins” headed by Prof. Wulf Blankenfeldt. The department focuses on unraveling molecular mechanisms of uncharacterized processes in the metabolism, regulation and virulence of pathogenic microorganisms. About the institute More than 800 people work at the HZI, a research institution in the Helmholtz Association of German Research Centres funded jointly by the Federal Republic of Germany and the Federal State of Lower Saxony. The centre’s task is to undertake biomedical research in the field of infection biology to expand knowledge of the fundamental mechanisms behind medically relevant infectious diseases with the aim of providing the key for the development of new therapeutics and vaccines. The Department “Structure and Function of Proteins” offers excellent working conditions, state-of-the-art technical platforms and equipment (including bacterial, insect cell and mammalian protein expression systems; access to a rotating anode X-ray source and several synchrotrons, crystal imaging and liquid handling systems; biophysical characterization of proteins), a lively scientific community and excellent support for the development of personal soft-skills. Projects All projects in our department aim at the identification and elucidation of the molecular function and mechanism of uncharacterized genes in pathogenic microorganisms. A better understanding of these “white spaces” of the genome map will not only unravel interesting new molecular processes but also provide novel targets for pharmaceutical intervention. To achieve our goal, we employ a gamut of methods including – in addition to structural biology – microbiological, biophysical and metabolomic techniques. Because our department is also the prime partner for structural biology-related questions at the HZI, the Technical University of Braunschweig and the German Centre for Infection Research (http://www.dzif.de/en/) the successful candidate will have the opportunity (and is expected) to take leading roles within our existing and emerging collaborations. Prerequisites Candidates should hold a Ph.D. in a life sciences related subject at the time of their employment. They should have a strong background in all aspects of macromolecular crystallography, including techniques of recombinant protein production and biophysical characterization. Experience in handling and manipulating pathogenic bacteria (biosafety level 2) is a plus. The handicapped Qualified applicants with a disability will be given preference. Job details The position is available immediately for three years with a six month probation period. Salary is according to level E14 of the collective labor agreement for public service (TVöD). Application details Candidates are asked to submit a full CV including a publication list, a cover letter outlining their interest in this position, a brief summary of current and past research experience (max. 2 pages) and contact data of at least two referees. All documents and information should be provided in English or German. Applications should refer to code 05/2014 and be sent by 28.02.2014 to: Helmholtz Centre for Infection Research Dept. of Human Resources Inhoffenstraße 7 38124 Braunschweig Germany E-Mail: JobsHZI(a)helmholtz-hzi.de For further information, please contact Prof. Dr. Wulf Blankenfeldt, phone: +49-531-6181-7000, e-mail: wulf.blankenfeldt(a)helmholtz-hzi.de ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie" Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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Re: [phenixbb] measuring the angle between two DNA duplexes
by Xiang-Jun Lu 26 Jan '14

26 Jan '14

Hi Xiang, Since you mentioned "or in other software", I think I can chime in to this topic. The short answer is to see "How to calculate DNA bending angle?" ( http://forum.x3dna.org/faqs/how-to-calculate-dna-bending-angle/). 3DNA, following the original NewHelix algorithm, calculates a best-fitted linear global helix (where sensible) using equivalent C1'...C1', RN9/YN1...RN9/YN1 atom pairs along each strand. The so-called global helical axis parameters are no longer widely used, but the best-fitted linear helical axis is a useful concept, and has been kept in 3DNA and DSSR [ http://forum.x3dna.org/rna-structures/dssr-software-for-defining-the-(secon… ]. HTH, Xiang-Jun -- Xiang-Jun Lu (PhD) Email: xiangjun(a)x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/ > > > On 1/20/14, 5:48 AM, ?? wrote: > > > > Hi, > > > > I have a DNA model which is composed of two DNA duplexes. I want to > > measure the angle between the two duplexes and if there a way to do it in > > PHENIX or in other software? > > > > Thanks you very much for your help! > > > > Sincerely, > > Xiang > > > > -- > > Li Xiang > > Department of chemistry, > > Purdue University > > Email?lixiang1642(a)gmail.com > >

2 1

non-bonded
by Leonard Thomas 23 Jan '14

23 Jan '14

Hello All, We are trying to refine a complex that was solved using Phaser. We have run a round of rigid body refinement using Refmac and now want to run a simulated annealing run in Phenix. Visually the complex looks pretty. The resolution we currently are at is 3.6 A. When we go to run phenix.refine the program quits with a Number of non-bonded interactions < 0.0001 error. Is there a way to loosen this up a bit or get around it or should we go about this in a different way? Best Regard, Leonard Thomas, Ph.D. Macromolecular Crystallography Laboratory Manager University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 Office: (405)325-1126 lmthomas(a)ou.edu http://barlywine.chem.ou.edu http://structuralbiology.ou.edu

3 2

measuring the angle between two DNA duplexes
by 李翔 22 Jan '14

22 Jan '14

Hi, I have a DNA model which is composed of two DNA duplexes. I want to measure the angle between the two duplexes and if there a way to do it in PHENIX or in other software? Thanks you very much for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

8 13

phenix.refine wxc weight
by rainfieldcn 18 Jan '14

18 Jan '14

Hi All, I am doing refinement on some low resolution structures ( around 4A ). I used wxc_scale=0.15 before on phenix.refine: 1.8.2_1309 I got: REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD MAX COUNT REMARK 3 BOND : 0.006 0.048 24993 REMARK 3 ANGLE : 1.049 11.841 33849 REMARK 3 CHIRALITY : 0.044 0.323 3843 REMARK 3 PLANARITY : 0.005 0.053 4276 REMARK 3 DIHEDRAL : 14.080 87.581 8889 REMARK 3 MIN NONBONDED DISTANCE : 2.098 REMARK 3 MOLPROBITY STATISTICS. REMARK 3 ALL-ATOM CLASHSCORE : 10.49 REMARK 3 RAMACHANDRAN PLOT: REMARK 3 OUTLIERS : 0.10 % REMARK 3 ALLOWED : 3.84 % REMARK 3 FAVORED : 96.06 % REMARK 3 ROTAMER OUTLIERS : 3.87 % REMARK 3 CBETA DEVIATIONS : 0 now, phenix is updated to phenix.refine: 1.8.4_1496. and I got: REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD MAX COUNT REMARK 3 BOND : 0.016 0.237 24993 REMARK 3 ANGLE : 2.262 36.773 33853 REMARK 3 CHIRALITY : 0.099 2.724 3847 REMARK 3 PLANARITY : 0.010 0.102 4280 REMARK 3 DIHEDRAL : 14.585 89.962 8889 REMARK 3 MIN NONBONDED DISTANCE : 1.923 REMARK 3 MOLPROBITY STATISTICS. REMARK 3 ALL-ATOM CLASHSCORE : 17.57 REMARK 3 RAMACHANDRAN PLOT: REMARK 3 OUTLIERS : 0.32 % REMARK 3 ALLOWED : 4.07 % REMARK 3 FAVORED : 95.61 % REMARK 3 ROTAMER OUTLIERS : 4.22 % REMARK 3 CBETA DEVIATIONS : 39 So I am wondering if there is some bug in phenix.refine that wxc_scale doesn't work? Thanks, Lei

2 1

MR
by Swastik Phulera 17 Jan '14

17 Jan '14

Dear All, I am trying an MR, it looks like there would be 16 dimers in the asymmetric unit, Upon running Phaser once it could easily fit two copies. I now wish to use this solution to perform further MR runs in order to locate the other dimers. I was just wondering what shall be the right way to go about it. Regards Swastik

4 4

Re: [phenixbb] phenixbb Digest, Vol 98, Issue 2
by Kay Diederichs 14 Jan '14

14 Jan '14

Am 14.01.14 21:00, schrieb phenixbb-request(a)phenix-online.org: > PS. It's possible I'm still misunderstanding the meaning of FRIEDEL'S_LAW=TRUE. > Under what circumstances does XDS output anomalous vs. non-anomalous data? This keyword affects the way the statistics are calculated in CORRECT.LP: with FRIEDEL'S_LAW=FALSE the members of Bijvoet pairs are treated as separate reflections, which almost doubles the number of unique reflections, affecting the reported completeness and R-values, I/sigmas and so on. The reflection output file XDS_ASCII.HKL has unmerged intensities in all cases (whether FRIEDEL'S_LAW=TRUE or FALSE). Phenix should ignore the FRIEDEL'S_LAW setting in XDS_ASCII.HKL. hope this helps, Kay

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XDS data
by Tim Gruene 14 Jan '14

14 Jan '14

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, I would like to run Phaser-EP through the phenix GUI. When I first uploaded the XDS_ASCII.HKL file, there was an error message about "No valid observed reflections found in this file". Subsequently I uploaded an unmerged hklf4 file. The GUI tells me I need to let phenix know about it being hklf4 by appending '=hklf4'. However, when I do so, there is an error message the file did not exist and the Data file line goes red. Where should I correctly append '=hklf4'? At the bottom, the message states it would be best to recover the original reflection data such as [...] XDS [...]. This suggests that the original XDS_ASCII.HKL could be used. Is this correct in if so, how do I put it into phenix? Best, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFS1TDEUxlJ7aRr7hoRArKdAKDpXBrs4wsWMvWw0JNo8F746fY76ACfeFuG geGY6T6se8peE9dEGz8ETow= =AaLk -----END PGP SIGNATURE-----

3 6

Refining coordinates
by Subhani Bandara 10 Jan '14

10 Jan '14

Dear all, I have a protein crystallized with metal chelate complexes and some of the atoms of chelators and the metals sit on the two fold axis. Is there a way that I can refine the coordinates of those atoms only along the two fold axis (let's say X) while restraining the coordinate refinement along other two axes (Y and Z)? Thanks Subhani

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fwd: Announcement: International Summer School of Crystallography - May 2014, Hamburg, Germany
by Nathaniel Echols 10 Jan '14

10 Jan '14

---------- Forwarded message ---------- From: "Oberthuer, Dominik" <dominik.oberthuer(a)cfel.de> To: phenixbb(a)phenix-online.org Date: Fri, 10 Jan 2014 16:14:08 +0100 Subject: Announcement: International Summer School of Crystallography - May 2014, Hamburg, Germany Dear colleagues, we are pleased to announce the first International Summer School of Crystallography at the Center for Free-Electron Laser Science at DESY, Hamburg (D). As part of the International Year of Crystallography 2014, Prof. Carmelo Giacovazzo will give a full week of lectures on the basics of crystallography, as well as the basics of modern phasing methods in protein crystallography. The course will cover basic mathematical understanding of crystallographic point and space groups, diffraction experiments, structure factor calculations, systematic absences, determination of space groups and many additional topics. After the discussions of theory, one afternoon will be spent to learn about modern applications of protein crystallography using advanced light sources, such as 3rd generation synchrotron and XFELs. The course will be given mainly for PhD students working in the field of crystallography, but exceptions for motivated PostDocs and MSc students can be made. The course will mostly cover mathematical background of crystallography, hence we are looking for students, having a (bio)physics background. This will NOT be a workshop covering protein crystallographic programs but rather the theory behind those programs. The course will start Sunday (11.05.2014) around lunch and will end Saturday (17.05.2014) around lunch. The registration fee is 100 EUR per person including coffee breaks and lunch. Accommodations can be made at the DESY Guest House: 70 EUR per person for 7 nights (10.-17.05.2014). Application deadline will be 28th of February 2014 and notification of accepted applications will be sent during March 2014. The applications will be managed via the DESY Indico system: https://indico.desy.de//event/ISSC14 Applicants must provide a motivation letter, as well as a CV, directly to the organizer Cornelius Gati (cornelius.gati(a)cfel.de). Places and accommodation are limited to 30 students in total. Please contact Cornelius Gati regarding further questions ( cornelius.gati(a)cfel.de). We are looking forward to welcome you in Hamburg! -- Dr. Dominik Oberthür CFEL - Center for Free-Electron Laser Science Coherent Imaging Division and University of Hamburg Laboratory for Structural Biology of Infection and Inflammation Notkestrasse 85 22607 Hamburg Germany phone: +49 (0)40 8998 6394 dominik.oberthuer(a)cfel.de obertuer(a)chemie.uni-hamburg.de

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Low F-obs Values
by 张怀东 07 Jan '14

07 Jan '14

Hi, everyone I used phenix-1.8.2-1309 to do MR and Autobuild, then Refinement, the max F-obs value of the mtz file from refinement was about 300. However, I used phenix-1.8.4-1496 to do the same work, the max F-obs value was about 3000. The resulting structure models donot seem to be any different. We tried several datasets of different proteins, and the max F-obs value are low with phenix-1.8.2-1309. So is this a real problem or not? Best regards Huaidong Zhang

2 1

I remind you: Please apply for RapiData 2014, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 06 Jan '14

06 Jan '14

We are offering RapiData 2014, the sixteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 27 April - 2 May 2014: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. In addition to MX there will be opportunity for learning about correlated MX and spectroscopy, and SAXS. You'll find the application materials on the Course Application tab at this site. For the twelfth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 27 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be an additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (no more than 30 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply yourself, or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Photon Sciences and Biosciences Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

1 0

Postdoc positions (SGC, Diamond): fragments into crystals
by Frank von Delft 02 Jan '14

02 Jan '14

Hello, I have 3 open postdoc positions, to work on technologies around fragment screening in crystals, which is what my (joint) research team at Diamond (beamline I04-1) and SGC (PX group) is trying to make simple and accessible. Details of the project are on my website <http://www.thesgc.org/scientists/groups/oxford/crystallography>; we need smart people to: * (at SGC) test-drive with start-to-end soaking campaigns <http://www.thesgc.org/careers/oxford/crystallography-postdoc-fragment-scree…> * (at SGC) develop crystal engineering to get soakable systems (molecular biology, biochemistry) <http://www.thesgc.org/careers/oxford/crystallography-postdoc-crystal-engine…> * (at Diamond) explore soaking techniques <http://www.diamond.ac.uk/Home/Jobs/Current/DIA0886_CH.html> The application deadlines for the SGC posts are a function of the UK's charming political climate; if you're interested but from outside the EU, alert me with a direct email plus CV. phx. P.S. if you know smart undergrads who'd be interested in a DPhil in that sort of thing -- applied engineering, technology -- send them to that website too. (DPhils are what you get in Oxford - that makes it special. Or "special".)

1 1

Multiple conformation, two ligands
by YANG HAI 01 Jan '14

01 Jan '14

Dear Phenix Community, I tried to model two ligands one of which has two conformations. In other words, the two scenarios are: 1) ligand X with conformation A (XA, 75% occupancy); 2) ligand X with conformation B (XB, 25% occupancy) plus another ligand Y. However, the problem is ligand Y will have steric clash with ligand XA. If I rename ligand X and Y to the same residue name then I do not know how to define the CIF file. I apologize if this question was asked before and I do not know how Phenix or other refinement can deal with multiple conformation a group of ligands. Thanks. Happy new year! Yang Hai Christianson Lab University of Pennsylvania

3 2

phenix morph- no shift problems
by Ming Sun 29 Dec '13

29 Dec '13

Hi Everyone I'm currently trying running phenix.morph model on a large complex. However, after 5 cycles of running, there were no shift at all. And we set data, model, map_coeffs, reference_restraints, morph_main.. Does anyone happen to have similar issues? Any specific parameter I should change? Thanks again -Ming

2 1

Reduce NQH
by jp d 20 Dec '13

20 Dec '13

hi, we were going through the logs recently and see something odd during Reduce N/Q/H analysis the log file looks like this: ================================== NQH flips ================================== r_work=0.3047 r_free=0.3518 Analyzing N/Q/H residues for possible flip corrections... segID AL01 renamed chain A for Reduce N/Q/H analysis segID AL02 renamed chain B for Reduce N/Q/H analysis ... segID AL29 renamed chain Y for Reduce N/Q/H analysis segID AL30 renamed chain Z for Reduce N/Q/H analysis segID AL32 renamed chain a for Reduce N/Q/H analysis segID AL33 renamed chain a for Reduce N/Q/H analysis segID AL34 renamed chain b for Reduce N/Q/H analysis segID AL35 renamed chain b for Reduce N/Q/H analysis ... segID BL28 renamed chain z for Reduce N/Q/H analysis segID BL31 renamed chain z for Reduce N/Q/H analysis segID BL13 renamed chain AA for Reduce N/Q/H analysis segID BL29 renamed chain AB for Reduce N/Q/H analysis ... we noticed that the lower case chain letters start to duplicate themselves and are not unique to each segid. when it starts the two letter chain, everything seems unique again. forgive me if that is expected, it just seems kind of strange this was seen in mutlple log files and we are using version Version: 1.8.4 Release tag: 1496 if you need our files or more details, let me know thanks jpd

2 2

ensemble refinement rfree values
by Arjun Raman 20 Dec '13

20 Dec '13

Dear Phenix Guys, I have recently been trying my hand at the ensemble refinement option in phenix.refine. I generally observe an increase in rfree after performing the ensemble refinement with a well refined (using anisotropic B) structure, but the r-free increases are fairly small. For instance, 18.53% to 18.9% (1.8 Angstrom structure) or 20.45% to 21.1% (1.9 A)...I understand what this technically means (the ensemble refined model isn't as good) but given the noise in the calculation due to the limited number of reflections for the test set (~1000), would someone consider these rfree increases significant? My apologies if this question is a well-answered one...I can't seem to find much discussion about the range of rfrees to be expected or whether a 0.3-0.5% increase is large enough to toss out the refinement. Normally, I would take the lower rfree but because the ensemble refinement procedure gives potentially much more information, this seemed like a relevant question to ask. Thanks so much for your time, Arjun Raman Ranganathan Lab UT Southwestern ________________________________ UT Southwestern Medical Center The future of medicine, today.

3 2

MR-SAD, Yb, combined phases
by Joseph Noel 19 Dec '13

19 Dec '13

Hi All, I am carrying out a structure refinement using experimental phases combined with an MR solution. The experimental phases are being determined from bound Yb3+ cations and the data is collected at one of the Yb absorption peaks of 1.385 A. I do have a few questions about the heavy atom arrangement and then refinement. At this wavelength, I am also seeing peaks after running MR-SAD that are actually not the Yb cations but the sulfurs on several of the proteins Cys and Met residues. Should I try and change this "heavy atom arrangement" to include Yb and S before determining the final refined phases that I would like to then use as restraints during the structure refinement? If so, its not clear how to do this in Phenix without it finding additional sites that it attributes to Yb but which are actually sulfurs. For MR, this is an exact structure. All I am doing is using Yb which substitute for Mg coordination sites as a source of experimental phases to see how it improves refinement and maps. Second, when I do refine using the MLHL target function, I am finding quite a bit of excess positive density around the Yb sites. How do I try and account for this? I have attempted to take care of it with ADP and occupancy refinement but that doesn't seem to be enough. The resolution is 2.2 A and the anomalous signal is quite good (alas that is why I am also seeing the sulfurs clearly in the anomalous difference map). Do I need to change the scattering table since the structure now includes at least 4 Yb cations per asymmetric unit (one 550 amino acid residue protein per asymmetric unit - 68% solvent)? Is it important to refine the anomalous groups? For the latter, one can't refine with phase restraints (MLHL) and anomalous groups together. I have to choose one or the other - no phase restraints and anomalous groups refined, or experimental phase restraints and no anomalous group refinement. My goal is to use additional experimental measurements - amplitudes and phases to improve refinement, map interpretation and ultimately ensemble refinement. Any help, comments, criticisms, etc will be very appreciated! Happy Holidays! Joe ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

3 3

phenix.rosetta_refine on OS X?
by Ben Eisenbraun 19 Dec '13

19 Dec '13

4 5

Please apply for RapiData 2014, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 16 Dec '13

16 Dec '13

We are offering RapiData 2014, the sixteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 27 April - 2 May 2013: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. In addition to MX there will be opportunity for learning about correlated MX and spectroscopy, and SAXS. You'll find the application materials on the Course Application tab at this site. For the twelfth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 27 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be an additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (no more than 30 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply yourself, or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Photon Sciences and Biosciences Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

1 0

off topic - linux flavors for crystallography
by Todd Jason Green 12 Dec '13

12 Dec '13

Hello All- I have used a trusty box running fedora core 3 for nearly a decade and I am (finally) upgrading to a new workstation. In lieu of Nat's recent mention of new linux installers of phenix, I thought I would try to get a consensus on what linux flavor(s), I should consider installing on my new box. It will be used with emphasis on typical crystallography software including 3D graphics (3 GB NVIDIA Quadro K4000 card). If anyone would like to make a suggestion for an OS, I thank you in advance. Pointers to a web review can work too. Best- Todd

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cyclic peptide refinement
by wei xia 12 Dec '13

12 Dec '13

Hi, I am trying to refine a structure with a cyclic peptide ligand.I create a 'TRANS' link between the C-ter and N-ter residues of the cyclic peptide during refinement.But there is obvious no bond formed between the two residues in the refined structure.I checked the geo file and found that there are only angle restraints but no bond restraints between the two residuesAnyone can help me out?Thanks in advance! Wei P.S. refinement.pdb_interpretation.apply_cif_link { data_link = TRANS residue_selection_1 = chain D and resname MVA and resid 5005 residue_selection_2 = chain D and resname ARG and resid 5001 }

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phenix.find_ncs_from_density density_search.dump_ncs_density doesn't output mtz
by Francis Reyes 11 Dec '13

11 Dec '13

I'd like to see the region of my maps that obey the NCS operators and I was hoping for separate mtz's for each region given I had set density_search.dump_ncs_density = True. However, I'm not getting any output mtzs. Any ideas? Thanks, F --------------------------------------------- Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

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phenix.refine nproc
by de Waal, Parker 10 Dec '13

10 Dec '13

Hello Everyone, I recently compiled phenix 1.8.4-1496 on a CentOS 6.4 server and am having trouble using phenix.refine in parallel using the nproc flag which always runs as a single thread. Please find my input parameters here: https://gist.github.com/anonymous/13b9d4d39ed4d0c9622a I'm wondering if maybe OpenMP isn't configured properly on our server? Or maybe the correct version is not installed when I compliled phenix. If anyone has any input or experience with a problem such as this I would be extremely grateful. Cheers, Parker

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Spatial filtering
by Machius, Mischa Christian 06 Dec '13

06 Dec '13

Potentially silly question: is spatial filtering used for increasing contrast in electron density maps? Is it used for any other kind of data manipulation in macromolecular crystallography, e.g., diffraction data processing, density modification, etc. I'm a bit fuzzy on that subject, and so I said 'potentially silly', because it could be that such approaches are totally common but have different names (such as local averaging/scaling and so on). Many thanks in advance. Cheers, MM

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Submissions for next CCN newsletter
by Nigel Moriarty 06 Dec '13

06 Dec '13

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the January 2014 issue is 15 December 2013 but if you can send me an email we can make exceptions so you can use the holiday break to work on your drafts. 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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DEN refinement
by Scott Thomas Walsh 05 Dec '13

05 Dec '13

Dear Phenix Users, Is it possible to use NCS restraints in DEN refinement like we can do in regular phenix.refine refinement? Thank you for your help. Cheers, Scott ************************************************ Scott T. R. Walsh, PhD Assistant Professor University of Maryland IBBR/CBMG 3127E CARB-2 9600 Gudelsky Drive Rockville, MD 20850 USA phone: (240) 314-6478 fax: (240) 314-6225 email: swalsh12(a)umd.edu<mailto:[email protected]>

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