- phenixbb - phenix-online.org

mr_rosetta fragment_files by chain
by Perry, Kay H. 10 Nov '15

10 Nov '15

I am trying to run rosetta for a heterodimer with two different chains. I have the following commands, but in some subprocesses, I get the error message: Sorry: Sorry, need 2 fragment files (3 and 9 residues) for rosetta_rebuild I have the following in my script: fragment_files_chain_list=V \ fragment_files_chain_list=A \ fragment_files_3_mer_by_chain="orfx3_03_05.200_v1_3" \ fragment_files_9_mer_by_chain="orfx3_09_05.200_v1_3" \ fragment_files_3_mer_by_chain="orfx1_03_05.200_v1_3" \ fragment_files_9_mer_by_chain="orfx1_09_05.200_v1_3" \ Do I need to have the chain ID in the filename? Kay Kay Perry NE-CAT 9700 S. Cass Ave. Bldg. 436 E007 Argonne, IL 60439 630-252-0692

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error with phenix.refinine
by Maxime Cuypers 08 Nov '15

08 Nov '15

hi, i have the following error refining a neutron structure (no xrays data) with the latest builds (dev and official): it used to work perfectly and now it says: tried many things with my pdb yet to no avail. even archived runs do not work anymore. ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS <Bi-Bj> <B> WEIGHT TARGETS work free delta data restr 19.38 23.49 4.11 1.665 13.405 32.138 0.039 Traceback (most recent call last): File "/usr/local/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/command_line.py", line 162, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/driver.py", line 1532, in run call_back_handler = call_back_handler).result File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/strategies.py", line 201, in __init__ ion_placement_manager = ion_placement_manager) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/macro_cycle.py", line 117, in __init__ self.call(self.adp, "ADP refinement (reciprocal space)") File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/macro_cycle.py", line 143, in call func(prefix = prefix) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/macro_cycle.py", line 396, in adp log = self.log) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/adp.py", line 62, in run h_params = h_params) File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", line 232, in __init__ nproc = nproc) File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", line 337, in __init__ result = self.try_weight(weight, print_stats=True) File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", line 427, in try_weight minimized = self.minimize() File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", line 496, in minimize self.model.set_refine_individual_adp() File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/model.py", line 1523, in set_refine_individual_adp iselection = selection_iso.iselection()) RuntimeError: cctbx Internal Error: /home/builder/slave/phenix-nightly-intel-linux-2_6-x86_64-centos5/modules/cctbx_project/cctbx/xray/scatterer_flags.h(417): CCTBX_ASSERT(f.use_u_iso()) failure. any clue what is happening? thank you for your help, Maxime Cuypers

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Berkeley Server Downtime Cancelled
by Paul Adams 06 Nov '15

06 Nov '15

Dear Colleagues, I’m pleased to report that the scheduled power outage has been cancelled and will be rescheduled for a future weekend. Cheers, Paul -- 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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Trends In Initial Crystallization Screening
by Mustafa Koksal 06 Nov '15

06 Nov '15

Dear members of the crystallography community, I would like to assess the tendency/trend in our community to outsource initial crystallization screening experiments. Here, outsourcing refers to sending your protein/DNA/RNA sample to a service provider, who will set up crystallization experiments, take images of crystallization drops at various time points, make images available to you, and, if you require, send you the plate to retrieve any crystals. To do assessment, I prepared a short-answer questionnaire, which contains 10 questions and should take less than 5 minutes to complete. I especially encourage the new PIs and young researchers to complete the questionnaire. Could you please fill out the questionnaire at the following link? https://tr.surveymonkey.com/r/BVNCPVV In case you are unwilling to click links in e-mails, I also included the questions here. Please reply with answers in private to: mustafakoksal(a)iyte.edu.tr Thank you very much for your contribution. Mustafa Questionnaire: 1. Have you outsourced initial crystallization screening experiments in any of your projects before? Yes No 2. If you did, what format and type of experiment you used (choose all that apply)? 96 well/plate 384 well/plate 1536 well/plate Sitting Drop Hanging Drop Microbatch Other (please specify) 3. If you did, what price did you pay per 96-conditions? 4. If you did not, what prevented you from outsourcing (choose all that apply)? It is costly Shipping a sample is hard Privacy concerns I prefer to do it in my lab I do not think it is advantageous I do not have enough sample Other (please specify) 5. Would you be interested in outsourcing initial crystallization screening experiments in future? Yes No 6. If you are interested, which method would you prefer (choose all that apply)? Sitting Drop Hanging Drop Microbatch Counter Diffusion Other (please specify) 7. If you are interested, up to what price would you be willing to pay per 96-conditions? $1 $2 $3 $4 $5 $6 $8 $10 $12 $15 $20 $25 $30 $50 8. If you are interested, what would be your minimum-maximum throughput (# of 96-condition experiments per month)? Note: a 1536-condition experiment is 16 x 96-condition experiments? 1 - 2 2 - 4 4 - 8 8 - 12 12 - 16 16 - 32 32 - 64 32 - 128 More than 128 9. How much sample would you be willing to sacrifice per screening 96-conditions (please specify in micrometers)? 10. Would you consider international shipping of your sample for outsourcing? Do you have any other comments? End of Questions -- Mustafa Koksal Postdoctoral Fellow University of Pennsylvania Department of Chemistry Roy and Diana Vagelos Laboratories Office: 2090 IAST Office Phone: (215) 898-2227 Mobile Phone: (267) 319-6443 Mail Address: 231 S. 34th St, Philadelphia 19104, USA --

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(no subject)
by Nigel Moriarty 06 Nov '15

06 Nov '15

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the January 2016 issue is 18 December 2015 (with some leeway if you are still working on the text, especially as it can be polished over the break). The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. 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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ERRASER Updates
by Caleb Geniesse 05 Nov '15

05 Nov '15

Hi all, My name is Caleb and I am a research programmer in the Das lab who has taken over the maintenance of ERRASER. ERRASER (Enumerative Real-space Refinment ASsisted by Electron-density under Rosetta) is an application for improving RNA crystal structures based on Rosetta and Phenix. While benchmarking the current state of ERRASER, I uncovered some discrepancies in the clash scores and outliers of the resulting models (compared to the original benchmark in Chou FC et al., 2012). Accordingly, I've made some updates to the ERRASER code within Rosetta addressing these issues. *To avoid possible inaccuracies introduced by these bugs,* *all PHENIX-ERRASER users should download/install a weekly build of Rosetta 2015.35 (released Sept. 24, 2015) or later.* For more extensive PHENIX-ERRASER documentation and installation notes, please see: https://www.phenix-online.org/documentation/reference/erraser.html. Please let me know if you have any questions! All the best, Caleb Geniesse

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Berkeley Server Downtime
by Paul Adams 05 Nov '15

05 Nov '15

Dear Colleagues, as part of routine maintenance at our new building there will be a power outage to the Computational Crystallography Initiative server room. As a result several structural biology web services will be offline for a short while. These include: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) The servers will be shutdown at 5pm Pacific time on Friday November 6th. Services should resume by the evening of Sunday November 8th at the latest. During the downtime bug reports and emails requesting help should be queued and received by us once the servers are back online. We greatly appreciate your understanding, and hope that this doesn’t present too much of an inconvenience. Cheers, Paul -- 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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Modifying restraints for a single glutamate
by Eric Johnson 05 Nov '15

05 Nov '15

Is it possible to modify the restraints for single glutamic acid residue that forms an ester bond with a heme? Formation of the ester bond should lengthen the C - O bond length. Normal restraints distort the geometry of the covalent adduct. Thanks, Eric Johnson

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Installation problem
by Ricardo Padua 04 Nov '15

04 Nov '15

Hi all, I have the error below when trying to install Phenix in Centos6 running in a virtual machine (VMware workstation 12) in Win7 Enterprise. I've searched for this error in ccp4bb, phenixbb and google but nothing came out. Can anyone enlighten me? Best ========================================================================== Phenix Installation version: 1.10.1-2155 machine type: intel-linux-2.6-x86_64 OS version: 2.6.32-573.el6.x86_64 destination: /usr/local/phenix-1.10.1-2155 # of processors: 8 ========================================================================= Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 262, in <module> installer(sys.argv[1:]).install() File "/home/rpadua/.local/share/Trash/files/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 185, in install self.install_from_binary() File "/home/rpadua/.local/share/Trash/files/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 295, in install_from_binary self.reconfigure(log=log) File "/home/rpadua/.local/share/Trash/files/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 460, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/home/rpadua/.local/share/Trash/files/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py", line 81, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/usr/local/phenix-1.10.1-2155/base/bin/python /usr/local/phenix-1.10.1-2155/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/phenix-1.10.1-2155/build --command_version_suffix 1.10.1-2155 phenix phaser solve_resolve labelit' failed with exit code 127 Ricardo

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Formylmethionine
by mohamed noor 01 Nov '15

01 Nov '15

Dear all I am refining my model (1.8 A) where there is an excess density even after fitting the N-terminal Met. From Edman degradation data, the Met is actually an FME. However, only the density in one chain allows me to confidently place FME, and not for the other chain. The first chain also has a good enough density for me to be able to build all the residues in the protein except the last two at the C-terminus. So, do I model FME for both chains? Thanks. Mohamed

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a question on rotamer restraints
by Smith Lee 31 Oct '15

31 Oct '15

Dear All, When I run phenix.real_space_refine, in the rotamer restraints step I meet the following error message: RuntimeError: rotatable bond atoms CG1-CD (as defined by tardy-tree): no match in rotamer-info.tor_ids Will you please let me know how to overcome this error? Best regards. Smith

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CaBLAM validate - alternative output?
by Oliver Clarke 28 Oct '15

28 Oct '15

Hi all, I really like the idea of CaBLAM validate for model validation at low resolution based on the CA and backbone geometry, but the output is a little limiting - either text or kinemage right now. Would it be possible to create an output format that can easily be visualized (and turned into figures) in chimera, pymol or coot? Maybe a modified version of the input pdb with the CA/peptide outlier status mapped to the B-factor and occupancy columns? Cheers, Oliver.

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Restraining/constraining partial occupancy waters
by David Briggs 27 Oct '15

27 Oct '15

Hi PhenixBB. I have a very minor problem with partial occupancy waters moving out of density during refinement I have 2 structures, one apo structure (~1.3Å), one ligand bound (~1.5Å). The ligand binding site contains a Calcium ion. In the apo form there are 2 waters co-ordinating this Calcium. In the ligand bound form, these waters are replaced by oxygen atoms within the ligand. However, the ligand is only at 0.5 Occupancy as part of the ligand lies on a crystallographic two-fold axis. The ligand itself refines well with occupancy fixed at 0.5, and the Bs are sensible. In the 50% of the molecules which don't co-ordinate ligand, two waters must co-ordinate the calcium ion, and in keeping with this, we see that the electron density around these positions is greater than would be expected for the 50% occupancy ligand. So I added 2 0.5 occupancy waters to the model at these positions. However, when I run phenix.refine (refining XYZ, real space, occupancy, and individual Bs (isotropic for the ligand & waters - for the protein I use anisotropic Bs) these two 'ghost waters' move out of the electron density and their Bs increase massively. *My questions are:* Is there any way to restrain these waters to their apo positions? Is this the correct approach? I had initially thought that reference model restraints might be useful here, but if I understand correctly, reference model restraints cannot be applied to waters - Is this correct? If I cannot restrain the waters to the apo positions, would I be justified in fixing (constraining) them? This seems a little extreme and I am loath to do it, but given the isomorphous apo structure, I do have evidence that in the absence of ligand waters do take up these positions. Can anyone help? Cheers, Dave [image: David Briggs on about.me] David Briggs about.me/david_briggs <http://about.me/david_briggs>

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2nd International Conference on Image Analysis in Three-dimensional Cryo-EM, March 30-April 2 2016
by Cathy Lawson 24 Oct '15

24 Oct '15

Dear Crystallography List Members, I'm forwarding info about this upcoming conference on image analysis in 3D cryoEM on behalf of the organizers. [Also, while I have your attention, a reminder to participate in the ongoing EMDataBank map and model challenges, see http://challenges.emdatabank.org.] <http://challenges.emdatabank.org.]> > We are pleased to announce the 2nd International Conference on Image Analysis in Three-dimensional Cryo-EM, to be held at Granlibakken Conference Center, Lake Tahoe, California from March 30 to April 2, 2016 (http://ncmi.bcm.edu/cryoemsoftware-2016). The 2016 Symposium builds on our very successful previous meeting on the same theme in 2014. > The goal of the Symposium is to discuss state of the art image analysis approaches to tackle challenging biological problems and to identify current limitations and remaining problems in the field as currently practiced. The goal will be for developers in this area, both established as well as students/postdocs to discuss the detailed algorithms and methodologies in this field in greater technical detail than is possible at more general meetings like the GRC. The central premise is that gaining a comprehensive and quantitative understanding of highly sophisticated machines, complexes, and organelles of the cell requires the active, timely and coordinated development of complementary image analysis and data mining algorithm and approaches. We have recruited an outstanding panel of speakers (current agenda provided in the web site). > > > Sessions: > > * Handling Compositional and Conformational Variability > > * High Resolution Subtomogram Averaging and Related Techniques > > * High Resolution Single Particle Analysis > > * Resolution Assessment, Model and Map Validation > > * Data Storage Roundtable > > * Poster Talks > > All session will focus on interactive discussions with plenty of time for questions. We will also have a poster session, and selected posters will be invited to give short-format talks. The early registration deadline for this workshop ends in Jan 2016. Registration details can be found at http://ncmi.bcm.edu/cryoem-software-2016. > > > Dorit Hanein, CHAIR & Steven Ludtke, Co-CHAIR > > ORGANIZING COMMITTEE > > Wah Chiu, Ed Egelman, Ben Hankamer, Masahide Kikkawa, David Mastronade, Pawel Penczek, Henning Stahlberg, Fei Sun, Niels Volkmann >

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Raw data.....
by Jrh 24 Oct '15

24 Oct '15

Good morning Tim, Overnight thoughts: Another aspect that seems to me to be accelerating now is the use of the diffuse scattering in MX structure AND dynamics analysis. There are several really nice papers in the last year. I post this on the Phenixbb because the drive forward on this is linked to Phenix. My point obviously is that this involves the whole diffraction pattern. I recognise that raw diffraction data measured for 'conventional crystal structure analysis', to use a term, may not be ideal but nevertheless these papers show that analysis is developing and so, at the Beamline, if diffuse scattering is evident it seems to me not so burdensome to add a data sweep with stronger exposures and a smaller beam (ie to minimising obscuring the diffuse by the Bragg). Also, just to mention, to add to my last message to you, I could mention specifically the very important initiative taken by Wladek Minor at Virginia within the US Big Data new funding. He already has a portal to 2800 raw data sets. At Utrecht Loes Kroon Batenburg and Toine Schreurs have shown what can be done with personal weblinks to raw data these last three years. And of course the US Structural Genomics centres pioneered much of this too. Greetings, John Emeritus Prof John R Helliwell DSc_Physics FInstP FRSC FRSB Fellow of the ACA Emeritus Member of the British Biochemical Society School of Chemistry, University of Manchester, M13 9PL, UK.

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Positions at the NKI - Amsterdam
by Anastassis Perrakis 24 Oct '15

24 Oct '15

Dear all, Three positions are available in the group of Anastassis (Tassos) Perrakis at the Netherlands Cancer Institute. We are looking for: 1. A post-doctoral scientist to work on the European Horizon2020 project iNEXT (http://www.inext-eu.org <http://www.inext-eu.org/>), on collaborative research activities aiming to develop, establish and apply biophysical methodologies for enabling ligand and fragment-based inhibitor discovery (in collaboration with the teams of Jose-Antonio Marquez at EMBL-Grenoble and Frank von Delft at Diamond) and for studying macromolecular interactions in vitro and in vivo (in collaboration with the group of Jan Ellenberg at Heidelberg). The research theme for applying and testing these technologies will be in the area of mitotic kinases and in particular on the study of their regulatory/localisation domains (see Hiruma et al, Science 2015 and Nijenhuis et al, J Cell Biol 2013). 2. A scientific programmer to help further develop our ProteinCCD Java application (http://xtal.nki.nl/ccd <http://xtal.nki.nl/ccd>, Mooij et al, Nucleic Acids Res 2009) and the PDB_REDO web server (http://xtal.nki.nl/pdb_redo <http://xtal.nki.nl/pdb_redo>; Joosten et al, IUCrJ 2014), and deploy them in virtual research environments and cloud-based systems, within the WestLife Horizon2020 e-Infrastructures project. The candidate should also help maintain and further develop the (C++) code behind the PDB_REDO rebuilding applications (Joosten et al, Bioinformatics 2011; Joosten et al Acta Crystallogr D 2012). 3. A scientist with a background on Cheminformatics or (Structural) Bioinformatics, to develop further the PDB_REDO pipeline (see above) to handle automated ligand and fragment placement, refinement and validation pipelines, and to pro-actively participate in the scientific and technical development of PDB_REDO. The Netherlands Cancer Institute (http://www.nki.nl <http://www.nki.nl/>) is a center of excellence with a high standard of biological research and an interactive international atmosphere. It is located in Amsterdam, with all its cultural amenities, close to the Schiphol airport. The group of Tassos Perrakis, which also hosts the team of Robbie Joosten working in the PDB_REDO project, is closely associated with the neighbouring group of Titia Sixma. Both groups have an interest in structural studies coupled to functional analysis, combined with activities in method development for structural biology. Our department also hosts the "Protein Facility" with equipment that includes high throughput crystallisation and crystal visualisation robotics, an X-ray facility, Biacore surface plasmon resonance, isothermal titration calorimetry (ITC), microscale thermophoresis, thermal shift analysis, multi-angle laser light scattering (MALLS), versatile systems for fluorescence based equilibrium and transient state kinetics analysis (a versatile plate reader and stopped-flow), and operational facilities for E.coli, insect cells and mammalian cells based protein expression and purification. Computational facilities are locally available. The groups also share equipment and office space, and together with the group of Thijn Brummelkamp create a lively and highly interactive research environment. Applicants should write an e-mail including a CV, a short letter of motivation and names and addresses of scientists willing to provide a reference to a.perrakis(a)nki.nl <mailto:[email protected]>. Tassos Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

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Re: [phenixbb] [ccp4bb] Tantalum anomalous signal of a low-resolution SAD dataset with lattice-translocation disorder
by Christian Roth 21 Oct '15

21 Oct '15

Hi, difficult to say why it doesn't work. Generally as mentioned already automatic model buildíng will most likely fail at this resolution. However why do you think your sites are wrong? Ta-cluster are regular compounds and the sites should fit with the geometry of the cluster at least. Anyway, molecular replacement using anomalous differences and the cluster as search model might work in that case as well, if direct experimental phasing fails. Cheers Christian Am 21.10.2015 um 05:19 schrieb Shun Liu: > Dear CCP4 colleagues, > > We are working on a Ta6Br14 cluster-SAD dataset (4.3 angstroms) with lattice-translocation disorder (with a total Rmerge of 0.16). Both SHELXC and Xtriage gave the similar positive result about the anomalous signal (See below). > > ------------------------------------------------------------------------------------------------- > Resl. Inf. 9.58 7.61 6.65 6.04 5.61 5.27 5.01 4.79 4.61 4.45 4.31 > N(data) 1427 1410 1410 1409 1385 1452 1367 1399 1367 1395 1385 > <I/sig> 76.3 52.1 26.7 13.7 8.7 6.1 5.1 5.0 3.9 2.7 1.8 > %Complete 98.8 99.9 100.0 99.9 100.0 100.0 100.0 99.9 99.7 99.6 95.8 > <d"/sig> 11.67 9.67 6.12 3.73 2.50 1.59 1.21 0.99 0.84 0.79 0.68 > ------------------------------------------------------------------------------------------------ > unused: - 49.7669 [ 0/29 ] > bin 1: 49.7669 - 9.2629 [3086/3100] 0.8212 > bin 2: 9.2629 - 7.3599 [3031/3031] 0.7689 > bin 3: 7.3599 - 6.4318 [3073/3073] 0.5380 > bin 4: 6.4318 - 5.8447 [3071/3075] 0.2933 > bin 5: 5.8447 - 5.4263 [3054/3054] 0.1230 > bin 6: 5.4263 - 5.1067 [3070/3071] 0.0363 > bin 7: 5.1067 - 4.8512 [3038/3039] 0.0126 > bin 8: 4.8512 - 4.6402 [3028/3048] 0.0074 > bin 9: 4.6402 - 4.4617 [2955/3037] 0.0021 > bin 10: 4.4617 - 4.3078 [2730/3059] 0.0000 > unused: 4.3078 - [ 0/0 ] > -------------------------------------------------------------------------------------------------- > The Tantalum sites and the initial map seem ambiguous, with which automatic model-building failed. > I am wondering whether the lattice-translocation disorder of the dataset impacts the reliability of the anomalous signal, tantalum sites and the initial map. If it does, how can we decrease its impact? If it doesn't, is it possible to find the accurate Ta sites and generate an interpretable map suitable for model-building with this dataset? (After all, it has been reported that Ta sites can be found at 6A resolution.) > > Any suggestion and comment will be highly appreciated! > > Best, > Shun >

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Tantalum anomalous signal of a low-resolution SAD dataset with lattice-translocation disorder
by Shun Liu 21 Oct '15

21 Oct '15

Dear Phenix colleagues, We are working on a Ta6Br14 cluster-SAD dataset (4.3 angstroms) with lattice-translocation disorder (with a total Rmerge of 0.16). Both SHELXC and Xtriage gave the similar positive result about the anomalous signal (See below). ------------------------------------------------------------------------------------------------- Resl. Inf. 9.58 7.61 6.65 6.04 5.61 5.27 5.01 4.79 4.61 4.45 4.31 N(data) 1427 1410 1410 1409 1385 1452 1367 1399 1367 1395 1385 <I/sig> 76.3 52.1 26.7 13.7 8.7 6.1 5.1 5.0 3.9 2.7 1.8 %Complete 98.8 99.9 100.0 99.9 100.0 100.0 100.0 99.9 99.7 99.6 95.8 <d"/sig> 11.67 9.67 6.12 3.73 2.50 1.59 1.21 0.99 0.84 0.79 0.68 ------------------------------------------------------------------------------------------------ unused: - 49.7669 [ 0/29 ] bin 1: 49.7669 - 9.2629 [3086/3100] 0.8212 bin 2: 9.2629 - 7.3599 [3031/3031] 0.7689 bin 3: 7.3599 - 6.4318 [3073/3073] 0.5380 bin 4: 6.4318 - 5.8447 [3071/3075] 0.2933 bin 5: 5.8447 - 5.4263 [3054/3054] 0.1230 bin 6: 5.4263 - 5.1067 [3070/3071] 0.0363 bin 7: 5.1067 - 4.8512 [3038/3039] 0.0126 bin 8: 4.8512 - 4.6402 [3028/3048] 0.0074 bin 9: 4.6402 - 4.4617 [2955/3037] 0.0021 bin 10: 4.4617 - 4.3078 [2730/3059] 0.0000 unused: 4.3078 - [ 0/0 ] -------------------------------------------------------------------------------------------------- However, the tantalum sites we found and the initial map seem ambiguous, with which automatic model-building failed. I am wondering whether the lattice-translocation disorder of the dataset impacts the reliability of the anomalous signal, tantalum sites and the initial map. If it does, how can we decrease its impact? If it doesn't, is it possible to find the accurate Ta sites and generate an interpretable map suitable for model-building with this dataset? (After all, it has been reported that Ta sites can be found at 6A resolution.) Any suggestion and comment will be highly appreciated! Best, Shun

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Queueing system commands for parallel Phenix/Rosetta jobs
by Yonglin Hu 21 Oct '15

21 Oct '15

Hello All, We have setup a cluster with several executing nodes and we would like to run our Phenix/Rosetta molecular replacement jobs on the cluster. In the Job Control screen, I put "qsub -q all.q -o $HOME/log1 -e $HOME/log1" as command to use to run multiple jobs. But I am not sure what I should use for "queueing system commands". We are using SGE as the queueing system on our cluster. Any help would be greatly appreciated! Yonglin Hu

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on cif file
by Smith Lee 20 Oct '15

20 Oct '15

Dear All, My protein containing the ADP-AlF3-Mg. In the protein ADP-AlF3-Mg should be very close to each other so that they look like the ATP binding with the Mg. I have prepared the ADP.cif and the ALF3.cif, and have merged the 2 cif files with elbow.join_cif_files. However when I run phenix.real_space_refine with the merged cif file, there was a tendency that ADP, ALF3 and Mg separated from each other based on the map density, which seems did not comply with the prior knowledge on that ADP-AlF3-Mg should occupies the space of ATP-MG. Will you please advice how to have ADP-AlF3-Mg occupies the space of ATP-MG rather than separated by the refine? Best regards. Smith

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Re: [phenixbb] How to convert XDS_ASCII.HKL to MTZ
by Whitley, Matthew J 19 Oct '15

19 Oct '15

Hi Murpholino, I’m not sure if your Phenix commands are correct, but you might try using the program that comes natively with XDS for converting between file formats. That program is XDSCONV. (As a side note, I think that some of the XDSCONV functions require CCP4 to be installed, so if you don’t have CCP4 installed you might need to stick to converting with Phenix.) You can find step by step instructions for generating an MTZ file from XDS output under the “Typical Use” heading here: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xdsconv More info about XDSCONV: http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xdsconv_parameter… Good luck! Matthew On Oct 19, 2015, at 12:16 PM, <phenixbb-request(a)phenix-online.org> <phenixbb-request(a)phenix-online.org> wrote: > > Message: 5 > Date: Mon, 19 Oct 2015 11:16:17 -0500 > From: Murpholino Peligro <murpholinox(a)gmail.com> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] How to convert XDS_ASCII.HKL to MTZ > Message-ID: > <CAMdBu0Uejh0k+Wih1KaF+c=FRJ3fKg+LhQrfuGhUs1tJ8x8HwQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Just want to be sure. > I want to generate the mtz file for refinement. The last step of XDS leaves > me with intensities and space group 89. So I need > > phenix.reflection_file_converter --generate-r-free-flags > --write-mtz-amplitudes --mtz_root_label=FOBS --mtz=d01.mtz > --change-to-space-group=96 XDS_ASCII.HKL > > Is this right? > > Thanks again >

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How to convert XDS_ASCII.HKL to MTZ
by Murpholino Peligro 19 Oct '15

19 Oct '15

Just want to be sure. I want to generate the mtz file for refinement. The last step of XDS leaves me with intensities and space group 89. So I need phenix.reflection_file_converter --generate-r-free-flags --write-mtz-amplitudes --mtz_root_label=FOBS --mtz=d01.mtz --change-to-space-group=96 XDS_ASCII.HKL Is this right? Thanks again

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refinement of coordinated ions
by Irina PROKHOROVA 18 Oct '15

18 Oct '15

Hello, I have many Osmium ions in my structure. They have 6 coordinated ammonium groups and I would like to refine the B-factors for them: one B-factor for Os in each residue and one B-factor for all 6 ammonium groups in each residue. For this I have chosen *group_adp with following syntax adp { group_adp_refinement_mode = one_adp_group_per_residue \ two_adp_groups_per_residue *group_selection group = chain O and element Os group = chain O and element N } I wanted to refine only B-factor for Osmiums in this refinement. To avoid the bias from previously refined values of B-factor I presetted B-factors for all Osmiums to 50. As a result I got the change of B-factors for all residues in the model to the same value (which probably means that all model was refined as one group) and R-free increased from 0.25 to 0.34. What should be the correct syntax for this refinement? Should I also refine ions coordinates for a good refinement of B-factors? Irina

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Fw: on phenix.real_space_refine
by Smith Lee 18 Oct '15

18 Oct '15

Dear Pavel, On Oct 9, 2015 I have e-mailed to you my experience with 1.9-1692 and version 1.10 (and 1.10.1) on phenix.real_space_refine. Today I just completed another protein phenix.real_space_refine. For the following comparison runs, the initial model same, the map same, all 5 macro_cycles default run. For version 1.10.1, the results were as following, Map CC (whole unit cell)： 0.672Map CC （around atoms）： 0.761rmsd （bonds): 0.01rmsd (angles): 1.55All-atom clahscore: 39.27Ramachandran outlier: 0.98%Ramachandran allowed: 12.71%Ramachandran favoured: 86.31%Rotamer outliers: 0.91%C-beta deviations: 0 For version 1.9-1692, the results were as following, Map CC (whole unit cell)： 0.645Map CC （around atoms）： 0.687rmsd （bonds): 0.0071rmsd (angles): 1.15All-atom clahscore:16.88Ramachandran outlier: 2.00%Ramachandran allowed: 6.23%Ramachandran favoured: 91.77%Rotamer outliers: 0.05%C-beta deviations: 0 For the version 1.10.1 phenix.real_space_refine, the most unacceptable was on the clashscore, the whole refine process seems did not care on the clashcore refine at all. I am looking forward to getting an explanation from you on the causes of the difference for phenix.real_space_refine for the 2 versions, and the possible strategy we can take to eliminate the difference to get the acceptable results. Best regards. Smith On Friday, October 9, 2015 12:52 AM, Smith Lee <smith_lee123(a)yahoo.com> wrote: Dear Pavel， As I have told you, I have tried phenix.real_space_refine for 2 protein with version 1.9-1692 and version 1.10 (and 1.10.1) for many times, with cif or without cif, with or without annealing. The general feedback was that the version 1.9-1692 was much much better for the final analysis of the PDB given at the end of the run of the phenix.real_space_refine. Especially for clashing score, version 1.9-1692 can gave acceptable results (below 20 or around 20), but the clashing score given by the above 2 new versions of phenix.real_space_refine was very high (around 50 or 100). For C-beta deviations, the output by 1.9-1692 was also much better Before I have tried the other nightly built versions of phenix.real_space_ refine between version 1.9-1692 and version 1.10 (and 1.10.1) , all I gave acceptable output analysis (something like the Molprobity analysis at the end of the run). Thus may I ask the reason you have version 1.10 (and 1.10.1) phenix.real_space_refine was because you have realized that the result given by version 1.9-1692 was too satisfactory? One direct concern of me was that you have recommended not to use the old version phenix. But I cannot get the satisfactory result with the new version phenix.real_space_refine. The other concern of me was that, I have noticed there were publications In Nature and Science which wrote they use phenix.real_space_refine to got the results in Nature and Science. The Phenix they used should be the versions earlier than version 1.10. Considering what I mentioned above, the Nature and Science results may be not so correct, if new version of phenix was considered as much better than the old version. Thus am I the only user who communicated with you on the high clashing score given by the new version of phenix？Can you give some comments on what I mentioned above on the high clashing score given by the new version phenix.real_spac_refine? Best regards. Smith

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Visualise NCS operators
by Morris, Kyle 17 Oct '15

17 Oct '15

Dear Phenix community, After running $ phenix.find_ncs what would be the best way to visualise the operators found and detailed in the *.ncs_spec file superimposed on the map used in the search? Thanks for your help! Best wishes, Kyle

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