- phenixbb - phenix-online.org

Special position ambiguity
by R Sarath 06 Oct '15

06 Oct '15

Hi, I have to place two carbon atoms (C3 and C6 - in para positions) of a cyclohexane ring from a ligand in special positions (I4122 space-group), with C6' from the symmetry generated molecule overlapping on C3 of the ligand. Can someone please suggest me a way to do so. I tried changing the occupancies of C3 and C6 to 0.5. After refinement, I observe that they don't overlap but instead spoil the fitting of neighbouring atoms of the ligand. Thanks in advance, Regards,Sarath

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on ligand restraint
by Smith Lee 05 Oct '15

05 Oct '15

Dear All, Does phenix.refine can process some ligands without the process by eLBOW, for example ATP, ADP,etc? Smith

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Selection of Torsion NCS restraint groups
by Victor Xiao 04 Oct '15

04 Oct '15

Dear all, I have a protein-DNA structure that has six molecules in ASU. All six molecules share the same sequence and very similar structure. However, only three of them bind to DNA and conformations are slightly different from the other three. By default, PHENIX will consider six molecules into the same NCS group. Now I am trying to set up two NCS group, e.g. chain A,B,C are in one group (no-DNA), chain D, E, F are in another group (DNA-bound). So I did the following steps: 1. I used PHENIX GUI and go to 'Utilities' -> 'Detect NCS Groups'. 2. Put chain A, B, C in 'Torsion NCS restraint group 1'. 3. 'Add group' and put chain D, E, F in 'Torsion NCS restraint group 2'. 4. Click 'Update and exit'. However, after that, when I re-open 'Utilities' -> 'Detect NCS Groups', I found all six chains A-F are in group 1, and all six chains A-F in group 2. Did I do something incorrectly? Or any other suggestion for my purpose? Thank you! Best, Xiao

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Phenix eLBOW output cif missing Chi angle information
by Xiao Lei 02 Oct '15

02 Oct '15

Hi Phenix BB members, I tried to generate restraints of 3-METHYL-BETA-D-ASPARTIC ACID (PDB 3 letter code ACB, http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=ACB). I am using this as a template for D-iso-aspartic acid in my model because I can not find a 3 letter code for the exact D-iso-aspartic acid (I know for L-iso-aspartic acid the code is IAS but no code for D-iso-aspartic acid) I can search in Phenix eLBOW (Mac Phenix Version 1.10pre) with code ACB and I can find the code and right compound, I tried to generate restraints of ACB using eLBOW and I got a cif and pdb output of the compound. However when I import the compound into coot, delete the methyl group to make the compound a D-isoAsp, and click "edit chi angles", I receive an error: This residue does not have assigned torsion/chi angles". I do not know what I should do to fix the problem. I thought eLBOW would automatically generate Chi angles but actually it did not in my case. I appreciate if you have any input on this. [image: Inline image 1]

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Non crystallographic symmetry
by Reza Khayat 02 Oct '15

02 Oct '15

Hi, I need to use icosahedral symmetry to refine a virus crystal structure. Does phenix support 60 NCS matrices? If not, how should I go about recompiling the program so that I can have 60 NCS matrices? Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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on phenix.refine
by Smith Liu 30 Sep '15

30 Sep '15

Dear All, If my protein contains a metal ion (Mg2+ for example, do I need a cif for the metal for phenix.refine? If my protein contains another ligand, which server can produce the ligand PDB suitable for the eLBOW? If my protein contains 2 ligands, then do I need 2 cif files for the phenix.refine or the phenix.real_space_refine? I am looking forward to getting your reply. Best regards. Smith

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on Phenix10
by Smith Lee 28 Sep '15

28 Sep '15

Dear All, With the EM cryo data, I have compared the function of phenix.real_space_refine of Phenix10 and Phenix1.9-1692. For the Ramachandran favored, the new version is about 90%, the old version is about 92%. For the clashscore by Molprobity, the new version is about 30, the old version is about 20. Molprobity indicated the clashing atoms were systematically existing in the whole molecule, rather than on specific parts of the protein which may be indication of bad modelling. Clearly the clashscore of 30 is unacceptable. Will you please give some advise on how to improve the function of new version of Phenix, considering adding H was not suitable as for the resolution was poorer than 4.0 A? Smith

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Re: [phenixbb] Rosetta refine compilation issue Centos 7 (ludovic Pecqueur)
by Kay Diederichs 28 Sep '15

28 Sep '15

just a wild guess - could it be that, according to http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Phenix#Installa… the Phenix installer requires (on Fedora and RHEL) the openssl-devel and libXt-devel to be installed on the system ? HTH, Kay Am 28.09.15 um 03:24 schrieb phenixbb-request(a)phenix-online.org: > 8. Re: Rosetta refine compilation issue Centos 7 (ludovic Pecqueur) > > Message: 7 > Date: Wed, 23 Sep 2015 14:09:08 -0700 > From: Paul Adams <pdadams(a)lbl.gov> > To: ludovic Pecqueur <ludovic.pecqueur(a)college-de-france.fr> > Cc: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Rosetta refine compilation issue Centos 7 > Message-ID: <68387823-8DAE-4C7F-84DF-5D79D36A3AD0(a)lbl.gov> > Content-Type: text/plain; charset=us-ascii > > Hi Ludovic, > > the problems seem to occur when scons is called to compile Rosetta. I notice that the scons.py file uses the python that appears first in your path (#! /usr/bin/env python). Is it possible that this is a python that is broken in some way? > > Cheers, > Paul > >> On Sep 23, 2015, at 9:11 AM, ludovic Pecqueur <ludovic.pecqueur(a)college-de-france.fr> wrote: >> >> Dear Developers, >> >> I have a fresh Centos 7 system and after installing Phenix I wanted to compile the Rosetta.refine module. (Rosetta from source version 2015.31.58019) >> >> I have succesfully compiled Rosetta but when I try to build the dedicated Rosetta for Rosetta_refine with rosetta.build_phenix_interface after setting up PHENIX_ROSETTA_PATH and ROSETTA3_DB I get the following error message: >> >> [XXX@...]$ rosetta.build_phenix_interface nproc=6 >> False >> scons: Reading SConscript files ... >> Running versioning script ... Done. (0.1 seconds) >> Could not find platform independent libraries <prefix> >> Could not find platform dependent libraries <exec_prefix> >> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] >> ImportError: No module named site >> CalledProcessError: Command '['./update_options.sh']' returned non-zero exit status 1: >> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 172: >> main() >> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 163: >> SConscript("SConscript", "build") >> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614: >> return method(*args, **kw) >> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551: >> return _SConscript(self.fs, *files, **subst_kw) >> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260: >> exec _file_ in call_stack[-1].globals >> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConscript", line 28: >> subprocess.check_call(["./update_options.sh"]) >> File "/usr/local/PROGRAMS/XTAL/PHENIX/phenix-1.10-2155/base/lib/python2.7/subprocess.py", line 540: >> raise CalledProcessError(retcode, cmd). >> >> If you have any idea of what could cause the problem, I would welcome any suggestions. >> I updated Phenix and I could compile phenix.rosetta_refine without problems on Centos 6.7. >> >> Thank you very much for your time and help. >> >> Kind regards, >> >> Ludovic. >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >

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Rosetta refine compilation issue Centos 7
by ludovic Pecqueur 24 Sep '15

24 Sep '15

Dear Developers, I have a fresh Centos 7 system and after installing Phenix I wanted to compile the Rosetta.refine module. (Rosetta from source version 2015.31.58019) I have succesfully compiled Rosetta but when I try to build the dedicated Rosetta for Rosetta_refine with rosetta.build_phenix_interface after setting up PHENIX_ROSETTA_PATH and ROSETTA3_DB I get the following error message: [XXX@...]$ rosetta.build_phenix_interface nproc=6 False scons: Reading SConscript files ... Running versioning script ... Done. (0.1 seconds) Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site CalledProcessError: Command '['./update_options.sh']' returned non-zero exit status 1: File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 172: main() File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 163: SConscript("SConscript", "build") File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614: return method(*args, **kw) File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551: return _SConscript(self.fs, *files, **subst_kw) File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260: exec _file_ in call_stack[-1].globals File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConscript", line 28: subprocess.check_call(["./update_options.sh"]) File "/usr/local/PROGRAMS/XTAL/PHENIX/phenix-1.10-2155/base/lib/python2.7/subprocess.py", line 540: raise CalledProcessError(retcode, cmd). If you have any idea of what could cause the problem, I would welcome any suggestions. I updated Phenix and I could compile phenix.rosetta_refine without problems on Centos 6.7. Thank you very much for your time and help. Kind regards, Ludovic.

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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

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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.

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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

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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

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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 +++++++++++++++++++++++++++++++++++++++++++++++++++

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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

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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!

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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

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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]>

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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

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refining different enantiomers
by Joel Tyndall 10 Sep '15

10 Sep '15

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

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Phenix version 1.10 released
by Paul Adams 08 Sep '15

08 Sep '15

The Phenix developers are pleased to announce that version 1.10 of Phenix is now available (build 1.10-2155). Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Highlights for this version: CDL as the default protein restraints, tools for planning a SAD experiment and scaling/merging SAD data, refactored xtriage GUI, use of intensities in molecular replacement, occupancy refinement mode after MR to automatically prune the model, expanded real space refinement for cryo-EM (and X-ray) data, NCS constraints in refinement, improved rotamer fitting in refinement, improved and consolidated secondary structure restraints, validation of peptide planes, protein backbone validation using Cablam, structure search tool, updated feature enhanced map protocol, TLS analysis tools, new continuous integration build system (BuildBot), and many other new utilities and fixes. General: ======== - New continuous build system, Buildbot - New tools for planning and evaluating SAD data collection and SAD datasets - All command-line installers converted to Python - Removed dependency on Apple tools for Mac installer relocation - Improved geometry restraints: - Nucleic acids: basepair planarity, hydrogen bonding and stacking restraints - Angle and torsion restraints for disulfide bonds - Conformation-Dependent Library is now the default (cdl=True) - Automatic linking has been expanded with carbohydrate linking being the default in all applicable programs - Names and places of parameters controlling secondary structure, reference and NCS restraints were changed - NCS constraints ("strict" NCS) for refinement (phenix.refine and phenix.real_space_refine) - Applied to coordinates and ADPs - Option to refine NCS operators - Partial LINK records support: - only in phenix.refine, phenix.geometry_minimization & phenix.real_space_refine - output LINK records generated using automatic linking and applied .edits (LINK in input PDB file are ignored) - HELIX/SHEET records in input file will be preserved in output PDB file Graphical interface: ==================== - Integrated help browser now supported on Linux - Improved display of Xtriage results, with summary of problems with data - Support for 'within' syntax in graphical atom selections - Model Reconstruction GUI: new GUI for building complete asymmetric unit and biological molecules using MTRIX and BIOMT records, respectively, in the PDB file - New interface for phenix.anomalous_signal - New interface for phenix.scale_and_merge Refinement: =========== - phenix.refine - Optionally use AFITT for geometry restraints of ligands - mmCIF output now includes _refln.pdbx_r_free_flag tag to explicitly record original R-free flags (instead of implicitly in status tag) - Updated Phenix GUI to handle reorganization of NCS implementation - main.secondary_structure_restraints, main.ncs and main.reference_model_restraints parameters were removed - Improved rotamer fitting (faster, less outliers) - Bug fixes - phenix.real_space_refine: - rigid-body refinement with possibility to specify rigid groups - NCS constraints are used by default - NCS groups are found automatically, also can be specified manually - support for custom restraints - support for ligand CIF files - map can have any origin (non-zero), refined model is not shifted to zero origin - if CCP4 map is used resolution must be specified using “resolution" keyword - Enable reference model restraints, including restraining to self - Many bug fixes, many tests added - phenix.secondary_structure_restraints (proteins and DNA/RNA) - Three methods are available to annotate protein secondary structure - Protein secondary structure definition may be outputted as HELIX/SHEET records in PDB format - New algorithm to search for nucleic acid base pairs and stacked pairs. - phenix.rosetta_refine: - more options for map type for real-space refinement, including composit omit and feature-enhanced maps - partial support for ligands (requires separate parameter files) - phenix.tls_analysis: - Decomposition of TLS matrices into elemental rigid-body motions (axes and amplitudes of vibration and libration). Validate TLS matrices. - phenix.tls_as_xyz: - Explicit interpretation of refined TLS parameters by decomposing into elemental rigid-body motions and generating structural ensembles that are consistent with these motions - phenix.multistart_sa: - utility for running multi-start simulated annealing refinements with varying random seed - sample uncertainty due to stochastic effects - also performs map averaging - parallelizes across multicore systems or managed clusters Experimental Phasing and Model Building: ======================================== - phenix.xtriage: - refactored for greater modularity and consistency between command line and Phenix GUI - simplified and clarified feedback, including new summary panel - many bug and stability fixes from PDB-wide testing - detection of elliptical truncation - analyze completeness of anomalous vs non-anomalous dataset - phenix.plan_sad_experiment (new command, GUI and command-line): - Estimate the I/sigI for a dataset that will be necessary to solve a structure by SAD - phenix.scale_and_merge (new command, GUI and command-line): - scale one or more SAD datasets, optimally using unmerged original index data, to create a scaled, merged dataset and to estimate the half-dataset anomalous correlation - phenix.get_cc_ano (new command,command-line only): - Calculate the anomalous correlation between two datasets - phenix.get_patterson_skew (new command, command-line only): - Get the skew of an anomalous difference Patterson and the ratio of anomalous differences to anomalous error. - phenix.merging_statistics: - calculate CC(anom) for split half-datasets Molecular Replacement: ====================== - Phaser: - now allows direct use of intensities instead of amplitudes for molecular replacement - new treatment of effect of intensity measurement error introduced - improved handling of weak data in normalization and anisotropy correction - new occupancy refinement mode to retain or prune residues along a chain - highlights loops and domains that are likely to need major correction - automatically invoked if high TFZ-score solution rejected for bad packing - subgroups feature: Phaser lists possible subgroups of space group, and if twinning is suspected the space group can be set explicitly to one of its subgroups for a molecular replacement search. In this case, the data will be expanded to the unique set for the subgroup. - new "Search" panel GUI making it less confusing to define multicomponent searches - replacing "Composition" with "ASU contents" on the GUI - phased translation function can be used, even as part of MR_AUTO search - magnification factor (cell scale) can be refined for electron density as a model: useful when cryoEM image reconstructions serve as models - SAD likelihood now reported as log-likelihood-gain: positive number relative to null hypothesis - Phaser now prints out suggestion for number of copies related by successive application of NCS translations (TNCS NMOL parameter), if suggested value > 2 - fixed bug affecting xyz-values > 100 in PDB for substructure - various other bug fixes - phenix.find_alt_orig_sym_mate: - Created new alias, phenix.famos, which is an anagram of the acronym for find_alt_orig_sym_mate and is easier to remember for the commandline. - phenix.subgroup_symmetry_datasets: - Calculates all subgroup of the diffraction data, and outputs them on the conventional setting. Useful to explore options when multple twin laws are possible. - phenix.structural_domain_search: - Domain search program using an approach based on graph theory. Very quick and fairly accurate for simple problems. Validation: =========== - phenix.omegalyze: - Identify non-trans peptide bonds in proteins. Three categories of peptide bond geometry: trans, cis, and twisted (>30deg away from planar). - phenix.cablam_validate: - Validation of protein backbones now uses separate contours for trans-proline vs cis-proline. - phenix.molprobity: - incorporated RNA validation New commands: ============= - phenix.model_idealization (new command, command-line only): - phenix.plan_sad_experiment (new command, GUI and command-line): - phenix.scale_and_merge (new command, GUI and command-line): - phenix.get_cc_ano (new command,command-line only): - phenix.get_patterson_skew (new command, command-line only): Other: ====== - phenix.model_idealization (new command, command-line only): - Idealize geometry of the input model. Only secondary structure elements of proteins are currently supported. - phenix.structure_search Quickly find homologous structures for a given model. There is an option to compile and output a list of ligands found in structures of those homologs. - phenix.map_model_cc (and its synonym phenix.model_map_cc): Compute model-map correlation coefficient (map CC or RSCC). Output overall, per whole model, per chain and per residue CC. Input map needs to be CCP4 fromatted file. - phenix.fem: - various bug fixes - make using "maximal synthesis" the default (before "minimal synthesis" was the default) - current version obsoletes all previous versions - phenix.chains_as_models: Convert PDB file with multiple chains into PDB file with multiple models (MODEL-ENDMDL). - phenix.models_as_chains: Convert multi-model (MODEL-ENDMDL) file into one model file with each model assigned unique chain ID. - phenix.helix_sheet_recs_as_pdb_files: Split PDB file into several PDB files with each file representing HELIX or SHEET record found in PDB file header. - phenix.map_value_at_point: Output map values at specified (x,y,z) points in space. - phenix.map_box: Extract box around selected atoms with map. Output PDB with atoms in the box and map files in CCP4, X-plor and MTZ formats. - phenix.model_model_distances: Given two PDB files output distances per atom, residue, chain, model and overall. It is assumed (and asserted in the code!) that the amount and order of atoms in both files are identical. - phenix.simple_ncs_from_pdb: Tool to find NCS groups in PDB model. Available in previous versions. Major code re-write to improve re-usabiliy. For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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on "occupancies" in the phenix.refine GUI
by Smith Liu 07 Sep '15

07 Sep '15

Dear All, In my map for a specific HISresidue, it was rather clear the sidechain has 2 conformations. In my start modle, I only have the PDB for 1 of the 2 conformations of the sidechain. With "occupancies" clicked, the refined PDB still only contain the PDB for 1of the 2 conformations of the sidechain (occupancy is 1). Thus in order to have the GUI "occupancies" takes function, I need manually add the PDB for the conformation of the other side chain, am I right? If I am right，will you please show me an PDB example which contains the conformations for 2 or several sidechains of a residue, so that I can know how to edit this kind of PDB? Best regards. Smith

2 1

Transfer FreeR and FreeR test set flag value
by Matthew Chu 07 Sep '15

07 Sep '15

Dear All, I am trying to refine my model against a higher resolution dataset. My colleage's old-low resolution dataset was processed in HKL/scalepack and the FreeR was assigned by Phenix.reflection file editor, which I assume the test set was marked as "1". Now I got a new-higher resolution dataset, and plan to process it in XDS/Aimless. I want to transfer the FreeR set from his old mtz and also use his low res model for the new refinement. My question is, when I transfer the FreeR set from his old mtz with flag value as "1" in Aimless, is the flag value now "1" or "0" in the new mtz output by Aimless? Can Aimless recognize the FreeR flag from the old mtz which are marked as "1"? I also read an old post from Nat Echols in 2011: "For Phenix, 1 is test, 0 is work, but you could reverse this and it will still figure out what to do automatically", so does it mean it doesn't matter if the FreeR is "1" or "0" in the mtz from Aimless, if I use phenix.refine for my new dataset, Phenix can figure out which is the correct FreeR value? It's a mix of CCP4 and Phenix question, so I have crossed posted it in the CCP4bb as well. Many thanks, Matt

2 2

a question on phenix refine
by Smith Liu 05 Sep '15

05 Sep '15

Dear All, For the GUI of phenix.refine, if we click "Optimize X-ray/stereochemistry weight", it should optimize on how to part the weight between X-ray and stereochemistry. Then if we do not click "Optimize X-ray/stereochemistry weight", phenix.refine will do with whole weight from "X-ray" or whole weight from "stereochemistry"? I am looking forward to getting your reply. Smith

2 1

Space group
by mohamed noor 04 Sep '15

04 Sep '15

Dear all I processed my images in point group P 3 2 1. After running Phaser and building it, the space group was P 3(2) 2 1. However, the refinement is stuck with Rfree at around 35-38 % (data extending to 3.3 A). As I believe the R factor is a bit high, and I have a different crystal form in P4(2) 2(1) 2 with R free at 25 % for data to 3.8 A, I expanded it to P 1, redid Phaser searching for 48 copies. After refinement, the R free is at 38 %. For some reason, Zanuda/Refmac is not able to read my files. So I ran Xtriage instead: A summary of R values for various possible point groups follow. ------------------------------------------------------------------------------------------------------- | Point group | mean R_used | max R_used | mean R_unused | min R_unused | BIC | choice | ------------------------------------------------------------------------------------------------------- | P 3 | 0.000 | 0.000 | 0.271 | 0.000 | 3.521e+05 | | | C 1 2 1 (2*y,-x+y,z) | 0.423 | 0.423 | 0.200 | 0.000 | 1.763e+06 | | | P 1 | None | None | 0.219 | 0.000 | 1.056e+06 | | | P 6 | 0.242 | 0.423 | 0.200 | 0.000 | 1.365e+06 | | | C 2 2 2 (x+y,2*y,z) | 0.271 | 0.423 | 0.200 | 0.000 | 1.464e+06 | | | P 3 2 1 | 0.000 | 0.000 | 0.423 | 0.423 | 1.761e+05 | | | P 3 1 2 | 0.242 | 0.423 | 0.200 | 0.000 | 1.365e+06 | | | C 2 2 2 (2*x,x+y,z) | 0.271 | 0.423 | 0.200 | 0.000 | 1.464e+06 | | | P 1 1 2 | 0.423 | 0.423 | 0.200 | 0.000 | 1.763e+06 | | | P 6 2 2 | 0.219 | 0.423 | None | None | 1.265e+06 | | | C 1 2 1 (x+y,-x+y,z) | 0.000 | 0.000 | 0.242 | 0.000 | 5.282e+05 | | | C 1 2 1 (x+y,2*y,z) | 0.423 | 0.423 | 0.200 | 0.000 | 1.763e+06 | | | C 1 2 1 (x-y,2*x,z) | 0.000 | 0.000 | 0.242 | 0.000 | 5.282e+05 | | | C 2 2 2 (x-y,x+y,z) | 0.271 | 0.423 | 0.200 | 0.000 | 1.464e+06 | | | C 1 2 1 (2*x,x+y,z) | 0.000 | 0.000 | 0.242 | 0.000 | 5.282e+05 | | | C 1 2 1 (x-y,x+y,z) | 0.423 | 0.423 | 0.200 | 0.000 | 1.763e+06 | | ------------------------------------------------------------------------------------------------------- R_used: mean and maximum R value for symmetry operators *used* in this point group R_unused: mean and minimum R value for symmetry operators *not used* in this point group Looking at the R values, it is possible that it is actually C 1 2 1. My questions: 1. What is the difference between the C 1 2 1 lines? What do the values in brackets mean? 2. Since Xtriage did indicate a possible NCS axis parallel to crystallographic axis (and it looks almost like that in my P321 model), do I reintegrate in one of those C121 and then redo Phaser/refinement? I can post a screenshot of model if that will help. Thanks. Mohamed

1 0

Positive density at metal ions
by Jan van Agthoven 03 Sep '15

03 Sep '15

Hi everyone, I work on a structure of about 3 A resolution. The structure is almost done except for 3 metal ions which remain positive in the density. The metal is clearly Mn (refinement works fine for an other very similar structure) and has been set at full occupancy. I tried to reset the B factor at lower values, which solves the problem for 2 metal ions but not the 3rd one. Is there anything else I can do? Jan

2 1

Rwork higher than Rfree
by Smith Liu 01 Sep '15

01 Sep '15

Dear All, Is poor resolution a factor leading to Rwork higher than Rfree? Any other factor? Best regards. Smith

1 0

Cell dimentions
by Bradley Hintze 30 Aug '15

30 Aug '15

Hello I have some interesting DNA structures I would like help with . The duplexes are stacked in the crystal head to head and tail to tail. This creates an interesting situation where an adenine is base pairing with itself across cell symmetry. The most likely way in which adenines base pairs with itself is if one is in the syn conformation and the other is in anti, i.e. a Hoogsteen base pair. However, that would break the symmetry as they are the same adenine and thus can't have two conformations. As such, I think it's appropriate to have two molecules, rather than one, in the asymmetric unit. I can make the new model easily enough by generating a symmetry mate and assigning different chain IDs but how do I appropriately calculate the new cell dimensions? Thanks, Bradley

2 1

on phenix refine of the cryo-EM data
by Smith Liu 29 Aug '15

29 Aug '15

Dear All, Phenix.real_space_refine can give nice results, but I still want to refine it by phenix refine graphical interface so that the refined PDB by Phenix.real_space_refine can have a much better resolution PDB from crystal structure as a reference PDB for further refine by phenix refine GUI, in case a fragment of the sequence may adopt a sheet structure as the reference structure, rather than a loop structure as obtained by Phenix.real_space_refine. When I use the phenix refine GUI for further refine, do I need to use electron scattering table, or I continue to use n-Gaussian scattering table? For the phenix refine GUI for this purpose, there will ne no necessity to click Optimized X-ray/sterochemistry weight and Optimize X-ray/ADP weight, as for it has no relationship with X-ray, am I right? The phenix.map_to_structure_factors converted mtz file, should correspond to the 2FoFcWT file. In the phenix GUI refine process, it will calculate the FoFcWT file. But each time I tried the refine by phenix GUI related to phenix.map_to_structure_factors converted mtz file, the signal of the FoFcWT file was almost as strong as or even much stronger than the 2FoFcWT file, which was in strong contrast with the phenix refine based on the crystal mtz file. Will you please explain why for phenix.map_to_structure_factors converted mtz file, phenix GUI can give such high signal of FoFcWT file? Best regards. Smith

1 0

off-topic: tenure track faculty position in cryo-EM
by Markus Seeliger 27 Aug '15

27 Aug '15

*Department of Pharmacological Sciences at **Stony Brook University * *Tenure-Track Cryo-EM Faculty Position in Conjunction with the Interdisciplinary Biomolecular Imaging Cluster Hiring Initiative* The Department of Pharmacological Sciences ( http://www.pharm.stonybrook.edu/faculty_research/overview) at Stony Brook University seeks applications for a tenure-track faculty position at the level of Assistant, Associate, or Full Professor. Candidates must have an M.D. and/or Ph.D., at least two years of postgraduate research experience, and an outstanding record of research accomplishment. This search is intended to recruit investigators with translational research programs that make use of Cryo-EM to pursue fundamental questions relevant to health-connected fields such as cancer, neuroscience, metabolism, and infectious disease. Senior candidates should have a record of success with extramural funding and training of students and/or fellows. Applicants must be eligible for a faculty appointment in accordance with the criteria established by the School of Medicine (Criteria for Appointment, Promotion and Tenure.) The Department has pre-doctoral and MSTP training grants, a broad infrastructure for research investigation, and newly renovated lab space housing structural biologists with expertise in NMR and x-ray crystallography. Many of the faculty use EM and Super-Resolution microscopy approaches, and additional structural biologists and imagers are found in the Departments of Biochemistry, Physiology, Chemistry, Microbiology, Neurobiology, and Biomedical Engineering. With the on-going NYSUNY 2020 Challenge Grant awarded to the University and the recent and largest gift ever to public higher education in the State of New York, Stony Brook University is embarking on a transformational expansion of the biomedical research enterprise. Diverse opportunities for collaborative research on campus include the Cancer Center, the Laufer Center for Physical and Quantitative Biology, the Center for Structural Biology, the Institute for Chemical Biology and Drug Discovery, and the interactive Computer Science and Applied Mathematics Departments. Imaging biological molecules is key to understanding their function, providing a starting point for rational drug design and protein engineering. Stony Brook University (SBU) is becoming a leader in biomolecular imaging through its newly-upgraded high-field NMR facilities including Bruker 700MHz and 850 MHz instruments with cryogenic probes, a strong program in computational structural and physical biology, world-class computational resources, facilities for radiotracer synthesis and human imaging, and proximity to the new third- generation synchrotron facility at Brookhaven National Lab (NSLS-II). The Biomolecular Imaging Cluster has already recruited junior faculty with expertise in x-ray crystallography and in super-resolution microscopy to add to our recent NIH-funded purchase of SIM and STORM instrumentation. *Most relevant to this recruitment, SBU received this year a $2M Shared Instrumentation award from NIH to obtain a state-of-the-art 200 kV Talos cryo-EM microscope and detector that will be installed and go live in Spring, 2016. * Stony Brook University, home to many highly-ranked graduate research programs, is located 60 miles from New York City on Long Island's scenic North Shore. Our 1,100-acre campus has more than 24,000 undergraduate, graduate, and doctoral students and 13,500 faculty and staff. The University is a member of the prestigious Association of American Universities and co-manager of the nearby Brookhaven National Laboratory, a multidisciplinary research laboratory supporting world-class scientific programs utilizing state-of- the-art facilities. Stony Brook University is also located close to the Cold Spring Harbor Laboratory with which it interacts through graduate program training and faculty collaborations. To apply, use Academic Jobs Online ( https://academicjobsonline.org/ajo/jobs/5904) to submit a State employment application, a complete curriculum vitae including publications, and a 3-page proposed research plan of current and future research, and have three letters of recommendation submitted through the AJO site. The cover letter should indicate whether the applicant wishes to be considered for appointment at the Assistant, Associate, or Full Professor level. Applicants at the Associate or Full Professor level should add a summary of past and current research funding and administrative and teaching experiences. *Electronic submission through AJO is required.* Questions should be addressed to Ms. Lynda Perdomo-Ayala, Department Administrator ( lynda.perdomo-ayala(a)stonybrook.edu, fax (631-444-9749.) POSITION OPEN UNTIL FILLED. For a full position description, visit www.stonybrook.edu/jobs (Ref.F-9530/15/08). Stony Brook University is an Affirmative Action, Equal Opportunity Educator and Employer.

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Re: [phenixbb] phenixbb Digest, Vol 117, Issue 9
by Cesar Santiago 27 Aug '15

27 Aug '15

Hi Mark! Anybody for the 24th trip to Alba? I'll be away from the 1st - 16th of September but I can still arrange the trip before leaving. César. ------------------------------------------------------------------ Cesar Santiago, Ph. D. Dept. of Macromolecules Structure at CNB, CSIC. X-ray Crystallography Facility. Campus Universidad Autónoma. Madrid, 28049 csantiag(a)cnb.csic.es On Aug 27, 2015, at 6:42 AM, phenixbb-request(a)phenix-online.org wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Re: phenix.refine automatic linking options (Engin ?zkan) > 2. external passive 3D monitor with macbook pro or imac for coot > and pymol stereo view (Xiao Lei) > 3. Rank-scaled map (Jianghai Zhu) > 4. Re: Rank-scaled map (Pavel Afonine) > 5. Re: on the starting mtz file for phenix refine (Pavel Afonine) > 6. Ligand addition in COOT for later refinement in Phenix.refine > (Manoj saxena) > 7. Re: Ligand addition in COOT for later refinement in > Phenix.refine (Oleg Sobolev) > 8. Computational Crystallography Newsletter - Volume 6, Number 2 > (Nigel Moriarty) > 9. Starting structure as reference model - crashing in 1.10-2142 > (Tristan Croll) > 10. Re: Starting structure as reference model - crashing in > 1.10-2142 (Pavel Afonine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 20 Aug 2015 15:41:31 -0500 > From: Engin ?zkan <eozkan(a)uchicago.edu> > To: Billy Poon <bkpoon(a)lbl.gov> > Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] phenix.refine automatic linking options > Message-ID: <55D63B7B.6000707(a)uchicago.edu> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > Dear Billy and Nigel, > > Thank you. Phenix.refine GUI in the latest nightly/release candidate no > longer has the master enable/disable button, and so the problem is resolved. > > Engin > > On 8/13/15 11:28 AM, Billy Poon wrote: >> Hi Engin, >> >> Thanks! We updated that part of the GUI so that it should be more >> intuitive. There is now a button that lets you apply automatic linking >> to all the components and a button that disables all automatic >> linking. You can, of course, still pick which components to enable by >> checking the specific boxes. >> >> On Tue, Aug 11, 2015 at 7:40 AM, Engin ?zkan <eozkan(a)uchicago.edu >> <mailto:[email protected]>> wrote: >> >> Dear Developers, >> >> Using the latest phenix nightly, I observed something odd in the >> phenix.refine UI, and I thought I should report it. If one >> unchecks Automatic ligand linking, this seems to not override its >> options, as the instructions in the Options window suggest. >> Specifically, if "Automatic Ligand Linking" is unchecked, but the >> "Link metals" is checked within its Options window, metal link >> restraints are still created. >> >> I checked the .geo file to confirm this. >> >> Thanks, >> Engin >> >> _______________________________________________ >> 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

Starting structure as reference model - crashing in 1.10-2142
by Tristan Croll 27 Aug '15

27 Aug '15

Hi, When I attempt to run a refinement in Phenix 1.10-2142 using the starting structure as a reference model, it crashes with the complaint that the reference (actually, the error states NCS - despite no NCS being present or enabled. I guess internally it's using the same code?) is too dissimilar to the model, and a calculated RMSD of >90 (degrees? I'm using torsion-angle restraints in any case). The same settings work without complaint on the same structure in dev-2006. I'm running from the GUI, checking "Reference model restraints" in the main phenix.refine window, and then "use starting model as reference" under "All parameters... Reference model restraints...". Thanks, Tristan

2 1

Computational Crystallography Newsletter - Volume 6, Number 2
by Nigel Moriarty 25 Aug '15

25 Aug '15

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. July 2015 <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf> Articles - A context-sensitive guide to RNA & DNA base-pair & base-stack geometry <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=22> Short Communications - New Phaser-MR search panel in Phenix <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=7> - Quantum chemical techniques for minimising ligand geometries in the active site <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=10> - 13 typical occupancy refinement scenarios and available options in *phenix.refine* <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12> Fitting tips #10 – How do your base pairs touch and twist? <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=3> 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

Ligand addition in COOT for later refinement in Phenix.refine
by Manoj saxena 24 Aug '15

24 Aug '15

Greetings I am trying to place a ligand (CIT) in a protein model that already have some citrate ligands placed. I am doing this using Coot's option "get monomer", and after the fitting of ligand in the density I tried to refine the model using the ligand and the protein pdb as input models. Refinement did not start and I got an error message in Phenix- "Number of groups of duplicate atom labels:....." Could someone please explain how could I get past this error message and what is the correct way to add a ligand to a model that already has some of the ligands of the same type. Many thanks in advance Regards Manoj Saxena

2 1

on the starting mtz file for phenix refine
by Smith Lee 22 Aug '15

22 Aug '15

Dear All, In the on-line phenix document, there is, "Should I use the MTZ file output by phenix.refine as input for the next round of refinement? The only time this is necessary is when you refined against a dataset that did not include R-free flags, and let phenix.refine generate a new test set. In this case, you should use the file ending in "_data.mtz" for all future rounds of refinement. You do not need to update the input file in each round, as the actual raw data (and R-free flags) are not modified". When we have phenic adding R-free flgas in the first time we process the mtz data by phenix.refine, besides the *data.mtz, phenix also create a *.mtz. In the future phenix.refine, can I refine by always using the *.mtz created in the R-free flag adding step, rather than refine by always using the *data.mtz created in the R-free flag adding step? What is the difference between that *data.mtz and that *.mtz? And what is the side-effect if in the future steps I refine by always using the *.mtz created in the R-free flag adding step? Best regards. Smith

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Rank-scaled map
by Jianghai Zhu 21 Aug '15

21 Aug '15

Hi, I know PHENIX can calculate a rank-scaled density map. Could anyone inform me which program in PHENIX actually does this? Thanks. Best, --Jianghai

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external passive 3D monitor with macbook pro or imac for coot and pymol stereo view
by Xiao Lei 21 Aug '15

21 Aug '15

Dear phenixbb members, I'm thinking to view stereo 3D structure on coot and pymol with passive 3D monitor, does anyone have experience of doing this with a macbook pro or imac and a external passive 3D monitor connected using HDMI port? If mac does not support this, should I buy a PC and a passive 3D monitor to do it? Thanks ahead. Xiao

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phenix.refine automatic linking options
by Engin Özkan 20 Aug '15

20 Aug '15

Dear Developers, Using the latest phenix nightly, I observed something odd in the phenix.refine UI, and I thought I should report it. If one unchecks Automatic ligand linking, this seems to not override its options, as the instructions in the Options window suggest. Specifically, if "Automatic Ligand Linking" is unchecked, but the "Link metals" is checked within its Options window, metal link restraints are still created. I checked the .geo file to confirm this. Thanks, Engin

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Phenix on Mageia
by Marie Elizabeth Fraser 19 Aug '15

19 Aug '15

Hello, We are having a problem getting the display of the cycles of Phenix running on our Linux machines. I am running Mageia 4, but the problem first appeared when I added a new student and he started to run Phenix on Mandriva. When I changed to Mageia 4, I had to do a clean install, so everyone got new home directories. Then the problem appeared for all of us. This has gone in as a bug report (and I can send the message if that would help). The response was that we were using a character like “é” in the filename or directory. I do not think that we are. However, at the bottom of the bug report it does say "LATIN CAPITAL LETTER A WITH RING ABOVE = Ã…”, which sounds like the symbol for Angstrom. Has anyone else seen a similar problem and been able to fix it? Thank you, Marie

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planarity between atoms of neighboring residues
by Agnieszka Kiliszek 19 Aug '15

19 Aug '15

Dear All, I would like to add restrains between two residues. I was trying to use geometry restrains planarity but I don't know how to select atoms from two different residues. I mean, I have: chain A resid 1 atoms: C5' C' and O1' chain A resid 2 atom: N1' I would like all 4 atoms to be planar. I found example only for atoms from the same residue. Can you help me? Agnieszka

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Re: [phenixbb] Different cell content than expected in Xtriage
by Singh, Bishal 19 Aug '15

19 Aug '15

Dear Folmer, Thank you very much for your words. Yes! I refined the model after molecular replacement. Electron density is nicely defined for all residues including their side chains. There is no extra electron density. All refinement parameters are fine. Rwork and Rfree are around 22% and 25%, respectively. The model that I used for phaser was a homology model generated from a structure with 60 % sequence identity to my protein. I prefer to use homology model than providing sequence identity in phaser because I think that the local structural errors are more precisely defined in homology models. Thanking you again! Kind regards, Bishal From: Folmer Fredslund <folmerf(a)gmail.com<mailto:[email protected]>> Date: Tue, 18 Aug 2015 15:34:23 +0200 To: noro <b.singh(a)dkfz-heidelberg.de<mailto:[email protected]>> Subject: Re: [phenixbb] Different cell content than expected in Xtriage Hi Bishal, Did you try to refine the model from phaser? Did you check the packing of the 2 molecules? Did you look at the electron density from phaser and see if some of it could look like an extra molecule? It is not impossible to have 70% solvent content, so I don't think you should be too worried, just investigate the result. You probably have another molecule there, phaser was just not able to find it, but you should be able to manually fit it easily. Btw, how similar is your model to your own protein? Hope this helps Folmer Fredslund 2015-08-18 15:02 GMT+02:00 Singh, Bishal <b.singh(a)dkfz-heidelberg.de<mailto:[email protected]>>: Dear all, I am solving crystal structure of a protein of size 33.7kDa in space group P 43 21 2 at 2.25 Å resolution. Unit cells constants are 121.51 121.51 156.6 90 90 90. The cell content analysis in Xtriage showed 1050 residues (~ 3X 33.7 kDa) per ASU with 50 % solvent content, whereas the molecular replacement in mr-phaser produced a dimer (2X 33.7 kDa). When we consider a dimer per ASU, it should have approximately 70 % solvent content. Please suggest me whether solution is right or not. I shall appreciate your opinions. Kind regards, Bishal _______________________________________________ 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]> -- Folmer Fredslund

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Coot mutation of Asp residue to isoAsp residue
by Xiao Lei 19 Aug '15

19 Aug '15

Dear Phenixbb members, I suspect one Asp residue in my model may be an isoAsp (isomerization of Asp). I am asking if there is way to mutate Asp residue to isoAsp(isoaspartic acid) residue in coot GUI (I'm using coot 0.8.1 EL in Mac OS X10.10.5)? I know there is a mutation button on coot, but the mutated aa lists are all natural amino acids. If I have to delete the Asp residue first and then build isoAsp into the density map, is there a way in coot to build an isoAsp residue in map? Thanks ahead. Xiao

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Different cell content than expected in Xtriage
by Singh, Bishal 18 Aug '15

18 Aug '15

Dear all, I am solving crystal structure of a protein of size 33.7kDa in space group P 43 21 2 at 2.25 Å resolution. Unit cells constants are 121.51 121.51 156.6 90 90 90. The cell content analysis in Xtriage showed 1050 residues (~ 3X 33.7 kDa) per ASU with 50 % solvent content, whereas the molecular replacement in mr-phaser produced a dimer (2X 33.7 kDa). When we consider a dimer per ASU, it should have approximately 70 % solvent content. Please suggest me whether solution is right or not. I shall appreciate your opinions. Kind regards, Bishal

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"Table 1" wavelength
by mohamed noor 17 Aug '15

17 Aug '15

Dear all A trivial question but just to be sure: For a structure phased and built using MR-SAD with a dataset collected at one wavelength and refined with a higher-resolution dataset at a different wavelength, how should the wavelength be reported in "Table 1"? And what if the higher-resolution dataset is not isomorphous to the anomalous dataset? Is it sensible to do MR-SAD first, redo MR with the better dataset against the MR-SAD model and then refine at the higher resolution (about 0.8 A better)? Thanks.

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Post-doctoral position in Structural Biology at the Goethe-University Frankfurt, Germany
by Maike Bublitz 14 Aug '15

14 Aug '15

Dear all, please find below a job announcement posted on behalf of my colleague Jun. Prof. Inga Hänelt at the Goethe-University Frankfurt: The Structural Biology of Membrane Transporters group of Inga Hänelt, Institute of Biochemistry at the Goethe University in Frankfurt am Main invites a post-doctoral researcher to join the Emmy Noether project “Determinants of ion channel versus transporter mechanism in the K(+) transporter superfamily“. The project is in need of a candidate with strong biochemical skills for membrane protein purification and/or experience in protein crystallization. If you are interested in further information please follow the link below. http://biochem.uni-frankfurt.de/fileadmin/user_upload/MechanismsMembraneTra… <http://biochem.uni-frankfurt.de/fileadmin/user_upload/MechanismsMembraneTra…> Contact Information for this post: Dr. Inga Hänelt Juniorprofessor for Biochemistry Institute of Biochemistry, Biocenter N220/1.03 Goethe-University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt Phone: 0049-69-798-29261 Fax: 0049-69-798-29495 Email: Haenelt(a)biochem.uni-frankfurt.de <mailto:[email protected]> -- Dr. Maike Bublitz Department of Biochemistry, Biocenter Goethe University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt am Main Germany phone: +49 (0)69 798 29274 bublitz(a)em.uni-frankfurt.de <mailto:[email protected]>

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on b factor refine for phenix.real_space_refine
by Smith Lee 14 Aug '15

14 Aug '15

Dear All, I first run a default phenix.real_space_refine with the map and initial model, with the model got, I run phenix.real_space_refine with run=adp, I find for the second phenix.real_space_refine step with run=adp, it can gives a reasonable value of b-factors for each residues in the model, and it cannot modify the coordinates of any atoms in the model (in comparison with the model got by the default phenix.real_space_refine in the first step). I just read a Nature paper from David Baker group "Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement", it says "Because cryo-EM maps are frequently better in resolution in some regions than others, atomic B factors are fit against cryo-EM density data to maximize the real-space correlation between model and map". For Real-space B-factor refinement, the math functions used by that Nature paper include, ( f is a scattering factor fit to each element) My question is, does b-factor refine only give a reasonable b-factor to each atom or residue in the model (so that we know the displacement of each atom or residue), or besides giving reasonable b-factor, it can also change and optimize the x y z coordinates of each atom in the model, and the phenomenon I observed in phenix.real_space_refine on that it only gives reasonable b-factor without modification of the x y z coordinates was only limited to the case I see in phenix.real_space_refine? Best regards. Smith

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Strong anomalous signal but AutoSol fails
by mohamed noor 11 Aug '15

11 Aug '15

Dear developers I have a low resolution anomalous dataset which Aimless suggests has an effective resolution to 3.3 A and anomalous signal to 3.5 A. However, SAD phasing with AutoSol is not successful with the final R factor around 50 %. I also have another dataset collected at a remote wavelength without anomalous signal to 3 A but they are not isomorphous (> 2 A difference in c axis). The anomalous signal comes from the ligand heme c, which is bound covalently to the protein, so its occupancy should be 1. The protein is quite small with about 120 residues. Xtriage suggests an NCS of 6 to 20 with most likely number to be 13. Is there any reason why a reasonable solution cannot be found? There is no twinning. I am using the latest nightly 1.10 pre2124. Thanks.

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ligand refinement
by xinghuaqin＠126.com 11 Aug '15

11 Aug '15

Hi everyone, I am refining a structure of protein/ligand complex (2.75 Å) almost to the last stage. However, I found that some atoms of the ligand is too close to the protein (1.2 or 1.3 Å) after refinement. How should I avoid this? Should I use the "nonbonded_distance_cutoff" parameter? What the value should be set to? Another question is that at this resolution is it possible for me to refine the occupancy? Any suggestion is appreciated. Best Xinghua Xinghua Qin Ph.D Department of Physiology The Fourth Military Medical University 169# Changlexi Road Xi'an 710032, China Tel. 86-29-84772779 E-mail: xinghuaqin(a)126.com

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Re: [phenixbb] anomalous difference map calculation
by Ashok Nayak 11 Aug '15

11 Aug '15

Alexandra Marques <at.marques(a)fct.unl.pt> wrote: >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb >Unsubscribe: phenixbb-leave(a)phenix-online.org

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Failed ADP refinement with active TLS and weight optimization
by Schubert, Carsten [JRDUS] 10 Aug '15

10 Aug '15

Hi, I am running into some strange issues with regards to ADP refinement especially when I am putting final touches on a structure for PDB submission. The problem manifests itself most prominent in the B-factor refinement of solvent, but also maps are affected and are becoming noisier, so I assume this problem affects the protein as well. I checked this against the current release 1.9 and the latest pre1.10 dev version, both versions show the issue. Refinement protocol includes individual_xyz, individual_adp, TLS and weight optimization. The problem I am running into is that the ADP of waters only changes by a global offset. The problem is tricky to spot but more evident when looking at solvent placed in coot with the default ADP (30). The ADP changes only by a global offset, no individual refinement takes place. Since the protein is refined by TLS the problem is not as evident, but as mentioned the fofc maps get noisier from cycle to cycle even though no manual change to the geometry was performed. To me an indicator that the B-factors are not refined properly. The problem can be circumvented by reverting back to isotropic B-factors and then refine with weight refinement for 5-10 cycles. After that TLS can be switched back on for a final polishing cycle. In stubborn cases I had to randomly assign B-factors close to Wilson-B and refine for more cycles to get out of the hole I refined myself into. Another indicator that something went awry is the weight refinement for the B-factors: ----------Individual ADP refinement---------- R-FACTORS <Bi-Bj> <B> WEIGHT TARGETS work free delta data restr 20.66 26.39 5.73 5.712 67.871 2.160 5.225 20.66 26.38 5.73 5.712 67.871 0.030 5.225 20.66 26.38 5.73 5.712 67.871 0.125 5.225 20.66 26.38 5.73 5.712 67.871 0.500 5.225 20.66 26.38 5.73 5.712 67.871 1.000 5.225 20.66 26.38 5.73 5.712 67.871 1.500 5.225 20.66 26.38 5.73 5.712 67.871 2.000 5.225 20.66 26.38 5.73 5.712 67.871 2.500 5.225 20.66 26.38 5.73 5.712 67.871 3.000 5.225 20.66 26.38 5.73 5.712 67.871 3.500 5.225 20.66 26.38 5.73 5.712 67.871 4.000 5.225 20.66 26.38 5.73 5.712 67.871 4.500 5.225 20.66 26.38 5.73 5.712 67.871 5.000 5.225 Essentially there is no change in R/Rfree with regards to different weights. I have not figured out the exact time point when this happens during the course of the refinement but it seems to be coupled to using TLS in combination with ADP refinement and during the final stages of the refinement. I can provide data offline to reproduce the issue Cheers, Carsten

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