- phenixbb - phenix-online.org

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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