- phenixbb - phenix-online.org

a question on phenix refine
by Smith Liu 23 Sep '15

23 Sep '15

Dear All, If my protein is rather large, and I have the mtz file of the whole protein, when I do phenix.refine of a single domain PDB of the whole protein against the whole protein mtz, after several cycles of phenix.refine the domain will not fit in the map at all (or even the domain moves far away from its initial position in map which it fits best), perhaps because the phenix.refine has made the domain to seek suitable fit in the map. Is any possibility at the whole process of phenix.refine we keep the domain relatively surround the map position where it fit best, so that phenix.refine will really do the refine in this situation? Best regards. Smith

1 0

ADP restraints under TLS+individual ADP
by Tristan Croll 23 Sep '15

23 Sep '15

Hi, When taking a structure I refined in Phenix (using a TLS + individual ADP model) into a different refinement package, a colleague noted a host of warnings related to mismatched B-factors between the sulfur atoms in disulfide bonds. If I understand correctly, this arises due to Phenix falling back to a Ulocal only ADP restraints scheme and, in particular, the choice to set adp_restraints.iso.sphere_radius = 2.0. The length of a disulfide bond being 2.05A, this means that as long as the geometry is correct the B-factors of the two sulfurs are never restrained to each other under these conditions. Cheers, Tristan Tristan Croll Lecturer Faculty of Health School of Biomedical Sciences Institute of Health and Biomedical Engineering Queensland University of Technology 60 Musk Ave Kelvin Grove QLD 4059 Australia +61 7 3138 6443 This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email.

2 1

labelit distl_minimum_number_spots_for_indexing
by Christian Roth 22 Sep '15

22 Sep '15

Dear Phenix-Team I installed the latest nightly build 1.8-1069. I tried to index some diffraction images and to overwrite the minimum usable spots for indesing I tried the suggested command. However If I try this command, it seems that it does not exist. At least in the list of the possible distl commands it does not show up. Do I have to install some additional stuff or change some preferences to get this command? Best Regards Christian

6 8

Alternative conformations in Coot
by Nigel Moriarty 21 Sep '15

21 Sep '15

Folks A recent article by Pavel Afonine in the Computational Crystallography Newsletter highlighted the flexible interface for alternative locations in Phenix. You can read it here: http://phenix-online.org/newsletter/CCN_2015_07.pdf#page=12 It recently came to my attention that some users who have an example of the Number 5 were having trouble viewing their models in Coot. After communicating with Paul Emsley, it turns out that you need a recent version of Coot (I ungraded from 0.8 to 0.8.2) and add the line allow_duplicate_sequence_numbers() to your ~/.coot.py file. You can test this using PDB 1ejg. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, 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

1 0

5'-phosphate group CIF files
by jens j birktoft 21 Sep '15

21 Sep '15

Hi everyone I need some suggestions for a CIF file for a 5'-phosphate moiety that is part of the nucleotide (CYT in this case) located at the start of a DNA strand (5' end) to be used in refinement in both PHENIX and COOT. All suggestions are appreciated. Cheers Jens -- +++++++++++++++++++++++++++++++++++++++++++++++++++ Jens J. Birktoft Structural DNA Nanotechnology New York University e-mail: birktoft(a)nyu.edu <jens.knold(a)gmail.com>; Phone: 212-749-5057 very slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 +++++++++++++++++++++++++++++++++++++++++++++++++++

3 2

why does "phenix generate table 1 for journal" plot stats different from those of XSCALE for example?
by Almudena Ponce Salvatierra 21 Sep '15

21 Sep '15

Hi everyone, I am trying to find out why phenix outputs differnt stats for the high resolution shell than XSCALE does. Anybody has observed this earlier? Best, Almu -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

3 2

3rd Annual Conference on the Biological Applications of X-ray Free Electron Lasers - BioXFEL
by Edward Snell 16 Sep '15

16 Sep '15

Dear all, This is not a directly related Phenix topic but the meeting may be of interest to Phenix users. Please note that the announcement also appeared on the CCP4 bulletin board with some incorrect spellings of names. I apologize to those concerned - my fault completely with travel, a high resolution laptop screen, and discovering I now need glasses to read at that resolution all to blame. The 3rd Annual Biological Applications of X-ray Free Electron Lasers (BioXFEL) meeting will be held at the Intercontinental Hotel in San Juan, Puerto Rico, from Jan 13th to 15th 2016. The conference is supported as part of the National Science Foundations BioXFEL Science and Technology Center, a consortium of eight US institutions headed by Ed Lattman and John Spence. The conference will focus on new and developing methods and biological results from biological XFEL research. The last day will cover hybridized developments capturing the growing interplay between XFEL and synchrotron sources. Confirmed speakers include Henry Chapman, Vadim Cherezov, Guillermo Calero, Marco Cammarata, Bob Fischetti, Helen Ginn, Heinz Graafsma, Abbas Ourmazd, Ilme Schlichting, Joerg Standfuss, and Rachel Woldeyes. Many others along with the preliminary agenda are to be announced shortly. The meeting will include education opportunities for post-doctoral and graduate students and an education and diversity talk by Cathy Drennan. A poster session will be held and a selection of abstracts submitted will be selected to be presented orally. The previous meeting of the series attracted over 150 international attendees with the talks, schedule, and environment stimulating much discussion and resulting in new collaborations. A diverse mixture of investigators from academic, industry and national laboratories will be present along with post-doctoral and graduate students. Anyone with an interest in this rapidly moving field is invited to attend. The registration fee is $300 (or $200 for students) with registration and details at https://www.bioxfel.org/events/details/64. Poster abstracts (with a preference for giving a talk if selected) should follow the format described on the webpage and be submitted by email to euppington(a)hwi.buffalo.edu. While the registration deadline is November 15th, the poster deadline is later, December 15th. However, talks will be selected from posters submitted from now until the registration deadline, until the presentation slots are filled. If you know of others who may not read the CCP4 board, please pass this information along. Come join us for a scientifically stimulating conference in a productive setting. Sincerely, Edward Snell and George Phillips (BioXFEL 2016 chairs) Edward Snell Ph.D. CEO Hauptman-Woodward Medical Research Institute Assistant Prof. Department of Structural Biology, SUNY Buffalo 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esnell(a)hwi.buffalo.edu Heisenberg was probably here!

1 0

2016 MicroED workshop at Janelia Research Campus
by Hattne, Johan 16 Sep '15

16 Sep '15

Janelia Research Campus (Ashburn, VA) will run a MicroED workshop February 22-25, 2016, hosted by Tamir Gonen. MicroED is a technique that uses electron diffraction to facilitate structure determination from sub-micron sized crystals, eliminating the need to grow large crystals. MicroED uses equipment and procedures that are standard on many cryo-TEM:s, and because of this the technique can be easily adopted in labs and facilities around the world. To encourage the widespread use of MicroED we are offering this workshop to teach microscopists how to perform the technique and adopt it at their own institutions. There is no registration fee for participation, and Janelia will provide on-site housing and meals. Attendees are expected to cover their own travel expenses and must be able to stay for the duration. Space in the course is limited. Those interested should send a brief statement on why they wish to participate to conference(a)janelia.hhmi.org by Friday, October 18. // Best wishes; Johan, on the behalf of the organizers Research Specialist @ Gonen Lab ____________________________________________________ Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

1 0

Re: [phenixbb] refining different enantiomers
by Joel Tyndall 13 Sep '15

13 Sep '15

Hi all, Just an update on the solution (which was to use the altloc). I needed to use a different residue numbers as well as different names all with an altloc flag e.g. AABA B 1 BABB B 2 CABC B 3 etc This way they were all recognised and were all maintained as different molecules with differing stereochemistry Thanks to all who gave help J From: Phan, Jason [mailto:[email protected]] Sent: Friday, 11 September 2015 8:05 a.m. To: Joel Tyndall <joel.tyndall(a)otago.ac.nz> Subject: Re: [phenixbb] refining different enantiomers J, I’d give it the same res num and chain id so the program won’t treat them as different residues. Don’t for get the altloc (AS3L and BS3L in my case). HETATM 1467 S19AS3L A 204 -5.833 10.423 7.671 0.62 23.15 S HETATM 1468 N20AS3L A 204 -3.414 9.416 7.552 0.62 24.27 N HETATM 1469 C21AS3L A 204 -3.040 10.374 10.388 0.62 29.37 C HETATM 1470 N22AS3L A 204 -2.138 10.275 11.024 0.62 30.28 N HETATM 1471 N01BS3L A 204 -4.128 11.351 13.823 0.38 32.89 N HETATM 1472 C02BS3L A 204 -4.731 10.188 13.418 0.38 32.83 C HETATM 1473 O03BS3L A 204 -4.635 9.141 14.001 0.38 34.60 O HETATM 1474 O04BS3L A 204 -5.450 10.323 12.316 0.38 28.92 O Jason On Sep 10, 2015, at 12:02 AM, Joel Tyndall <joel.tyndall(a)otago.ac.nz<mailto:[email protected]>> wrote: Hi all, I have a case where we have crystallised a ligand in our protein and the ligand purchased is a mixture of 4 structural isomers (enantiomers and diastereomers). There is no way of telling if one over the other is bound in the active site so we have assumed all 4 are binding. I have generated 4 separate ligands with 4 separate cifs and the all fit the density. I am refining the complex with all 4 ligands at 0.25 occupancy (occupancy refinement is switched off, I have changed the clash guard non-bonded distance threshold is set to 0.0 (as an initial error message came up with nonbonded interactions < 0.5). My refinement ran to completion, but something is definitely not right. The pdb file won’t load in Coot and in pymol the ligands have imploded/exploded. I am just wondering if this is the best way to refine this structure (or I have missed something) and probably more to the point what have I missed with the ligands. To me it is almost identical to alternate conformations, but I have obviously missed something I have just install phenix 1.10 on a windows machine. Thanks J _________________________________ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293 _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]>

1 0

Problem with mr_rosetta
by Kerff Fred 10 Sep '15

10 Sep '15

Hello, I’m trying to use mr_rosetta on my protein. I’m using OS X and upgraded phenix a couple of days ago and install rosetta at the same time. My job stops with the following message in this log file /phenix/MR_ROSETTA_52/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_6/WORK_1/rebuild.log. ERROR: can't find residue type at pos 1 in sequence ...sequence removed… ERROR:: Exit from: src/core/pose/annotated_sequence.cc line: 236 [35m0 mr_protocols.macosclangrelease 0x000000010b198bd6 print_backtrace() + 54 1 mr_protocols.macosclangrelease 0x000000010b198ab4 utility::exit(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int) + 804 2 mr_protocols.macosclangrelease 0x000000010a9b8ca1 core::pose::residue_types_from_sequence(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, core::chemical::ResidueTypeSet const&, bool) + 3697 3 mr_protocols.macosclangrelease 0x000000010a9ba6ea core::pose::make_pose_from_sequence(core::pose::Pose&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, core::chemical::ResidueTypeSet const&, bool) + 26 4 mr_protocols.macosclangrelease 0x0000000109267969 protocols::comparative_modeling::ThreadingJobInputter::pose_from_job(core::pose::Pose&, std::__1::shared_ptr<protocols::jd2::Job>) + 1449 5 mr_protocols.macosclangrelease 0x0000000109cb0c58 protocols::jd2::JobDistributor::run_one_job(std::__1::shared_ptr<protocols::moves::Mover>&, long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, unsigned long&, unsigned long&, bool) + 2232 6 mr_protocols.macosclangrelease 0x0000000109cafb5b protocols::jd2::JobDistributor::go_main(std::__1::shared_ptr<protocols::moves::Mover>) + 331 7 mr_protocols.macosclangrelease 0x0000000109c8d1f2 protocols::jd2::FileSystemJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 66 8 mr_protocols.macosclangrelease 0x00000001089e9964 my_main(void*) + 3124 9 mr_protocols.macosclangrelease 0x00000001089eae19 main + 4713 10 libdyld.dylib 0x00007fff8c8555c9 start + 1 11 ??? 0x0000000000000002 0x0 + 2 [0mError: ERROR: Exception caught by JobDistributor while trying to get pose from job 'S_PHENI_0001' Error: [ERROR] EXCN_utility_exit has been thrown from: src/core/pose/annotated_sequence.cc line: 236 ERROR: can't find residue type at pos 1 in sequence ...sequence removed... Error: Treating failure as bad input; canceling similar jobs protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: S_PHENI_0001 protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 15 jobs considered, 1 jobs attempted in 0 seconds caught exception 1 jobs failed; check output for error messages Anybody can help? Thanks Fred ----- Frédéric Kerff Chercheur qualifié F.R.S.-FNRS Cristallographie des protéines Centre d'Ingénierie des Protéines Université de Liège 17, Allée du 6 Août - Bat B5a 4000 Liège (Belgium) Tel.: +32 (0)4 3663620 Fax: +32 (0)4 3663772

1 0