- phenixbb - phenix-online.org

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

17 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 16 Feb '14

16 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 11 Feb '14

11 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 10 Feb '14

10 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 10 Feb '14

10 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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