- phenixbb - phenix-online.org

Phenix bug fix version 1.10.1 released
by Paul Adams 07 Oct '15

07 Oct '15

A bug fix version of Phenix is now available (build 1.10.1-2155). Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ This addresses the following issues: - Incorrect location used for heavy atom files when running AutoBuild in certain circumstances - Errors when adding hydrogens to waters in ReadySet - Errors when using GUI helper applications that handle sequences (e.g. Blast search) 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 Interim Division Director, Molecular Biophysics & Integrated Bioimaging, 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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Answer regarding uploading 2Fo-Fc map into KiNG
by Christopher Williams 06 Oct '15

06 Oct '15

Hi Natalia, Thanks for your use of MolProbity and your interest in improving models. It means a lot to us. As you have noted, MolProbity indeed does not accept .mtz files. It accepts 3 file formats for electron density maps: OMAP, CCP4, and XPLOR. Fortunately, Phenix can generate maps for you. In the Phenix GUI, there are two relevant options under the "Maps" tab. The first one, "Calculate maps", can turn structure factors into .mtz or .ccp4 . The second one, "FFT map coefficients", can use a .mtz to generate a .ccp4 or a .xplor, and is probably the option you are looking for. Someone more familiar with the Phenix commandline may be able to tell you how to generate maps from the commandline in a more scriptable way. Hopefully this helps, -Christopher Williams ---Richardson Lab, Duke University

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on cif file
by Smith Lee 06 Oct '15

06 Oct '15

Dear All, For the phenix refine of a protein-ligand complex, is the ligand cif file a necessity? If we do not add the cif file, what will occur? Best regards. Smith

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Special position ambiguity
by R Sarath 05 Oct '15

05 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

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