- phenixbb - phenix-online.org

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 16 Oct '15

16 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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Postdoctoral Position in Structural Biology at ICR, London, UK
by Sebastian Guettler 16 Oct '15

16 Oct '15

Dear PHENIX Community, Please see below for details of a postdoctoral position in our team. Best wishes, Sebastian Guettler Postdoctoral Position in Protein Biochemistry / Structural Biology / Electron Microscopy We seek to appoint a Postdoctoral Training Fellow to the research team led by Dr Sebastian Guettler in the Divisions of Structural and Cancer Biology at The Institute of Cancer Research in London, UK. The position is funded by Cancer Research UK. The successful applicant will undertake biochemical, structural and functional studies on members of the ADP-ribosyltransferase (or “PARP”) family of proteins and macromolecular complexes containing PARPs. Our goal is to gain insight into the control and cellular roles of these enzymes with a specific interest in ADP-ribosyltransferase-dependent signalling processes linked to cancer. Applicants should possess a PhD in a biological science such as biochemistry or molecular biology. Experience with recombinant DNA techniques, high-quality protein expression and purification, protein characterisation, structural biology, as well as some experience in structural electron microscopy are essential. Appointment will be on a Fixed Term Contract for 3 years in the first instance. The full salary scale is in the range from £29,517 to £42,187 p.a. inclusive. Starting salary will be based on previous postdoctoral experience. To apply, please submit your CV and covering letter online. Please include the names and addresses of two referees. For further details and instructions on how to apply, please refer to our online vacancy and recruitment site at http://www.icr.ac.uk/jobsearch, quoting job reference number 1494999 for this position. While applications need to be placed via our online system, informal inquiries can be sent to Dr Sebastian Guettler at sebastian.guettler(a)icr.ac.uk<mailto:[email protected]>. Please do not submit your formal application by email! Summary: Closing Date of vacancy: 31 Oct 2015 Type of Contract: Fixed Term, Postdoctoral Training Fellow Length of Contract: 3 years Salary Range: £29,517 p.a - £42,187 p.a. inclusive (full salary scale) Work Location: London Research in the Divisions of Structural and Cancer Biology focuses on the functional, biochemical, and structural characterisation of cellular processes relevant to cancer and cancer therapy. The Division of Structural Biology has managed state-of-the-art facilities for protein crystallography (crystallisation robots, Bruker Microstar and CCD detector), cryo-electron microscopy (FEI Tecnai F20 and T12), and protein production with expertise in multi-subunit expression (insect cell, yeast and bacterial expression, including a 60-litre fermentor). The Division is also well-equipped with instrumentation for biophysical analysis (e.g. ITC, fluorescence, multi-angle light scattering). The Division of Cancer Biology provides a state-of-the-art infrastructure for mammalian cell culture, imaging, mammalian genetics, chemical biology and proteomics. The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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Local B-factor for a ligand
by Karchevskaya, Anastasia 15 Oct '15

15 Oct '15

Dear Phenix users, Can you, please, clarify, how can I get local B factor for the residues around the ligand. 1) I saw this reply in an archive: http://www.phenix-online.org/pipermail/phenixbb/2011-March/016819.html 2) But it doesn't suit me, because, for instance in this case: http://www.rcsb.org/pdb/explore/explore.do?structureId=4RUP the interacting residues are: http://www.rcsb.org/pdb/images/H97:4RUP_psv_v_500.png 302, 265, 175, 423 can be fitted into a sequence, but I don't need everything in between them 3) There is also another option: http://www.ebi.ac.uk/thornton-srv/databases/PDBsum/ru/4rup/grow.out I can extract interactions from here and make a request to Phenix. If so, can I request the b-factor just for one exact amino acid? Thank you in advance, Anastasia

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peaks and holes for a difference map
by Murpholino Peligro 15 Oct '15

15 Oct '15

Hi. Is there a way to load a pdb and a difference map (ccp4 format) in phenix, command line is better, and then get something like the "validate->difference map peak" analysis (as in coot)..? Thanks

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MRC map as molecular replacement model
by Acharya, Priyamvada (NIH/VRC) [C] 15 Oct '15

15 Oct '15

Hi all, I want to use an MRC map obtained by low resolution EM reconstruction, as molecular replacement model in Phaser. I serached the phenixbb archives and learned that I should us phenix.map_to_structure_factors to convert the map file to mtz so it can be input into Phaser. When I do that I get an error "Sorry: Map must have origin at (0,0,0): recenter the map and try again". I have two questions? 1) What tool should I use to recenter the map and 2) Is there a better way to do this? Thanks in advance for your replies. Best regards, Priyamvada

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2016 MicroED workshop at Janelia Research Campus (Reminder)
by Hattne, Johan 15 Oct '15

15 Oct '15

Reminder: the deadline for applications for the workshop is this Sunday, October 18. The original announcement (minus a few typos) is included below. 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 Sunday, October 18. // Best wishes; Johan, on 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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Announcing the 2015/2016 EMDataBank Model Challenge
by Cathy Lawson 14 Oct '15

14 Oct '15

Dear PhenixBB List Members, EMDataBank is pleased to announce the 2015/2016 Model Challenge. All members of the Scientific Community--at all levels of experience--are invited to participate as Challengers, and/or as Assessors. Benchmark targets of varying size and complexity have been selected from recently deposited 3DEM structures based on current state-of-the-art detectors and processing methods, in the resolution range 2.2-4.5 Å. Challengers are sought to create and validate models from challenge target maps in four different categories (1. optimize current cryoEM model, 2. fit known related cryoEM, crystallographic, or comparative models, 3. ab initio model building, 4. any other method of map interpretation), and upload their results with associated details. Assessors are sought to participate in evaluating submitted models. Registration is now open for all interested participants. Challengers may submit their models between November and April. Before submissions open, all are encouraged to provide feedback on submission requirements. An open assessment period will commence in late 2016. To learn more about this challenge and to register, please visit http://challenges.emdatabank.org and click on "MODEL CHALLENGE" in the menu bar. This is the second of two community-wide challenges being sponsored by EMDataBank this year to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing validation criteria associated with every 3DEM map and map-derived model. The first challenge is focused on creating reconstructions from raw 2D image data and is currently in progress (click on "MAP CHALLENGE" in the menu bar). Sincerely, Cathy Lawson on behalf of the EMDataBank Team and the Model Challenge Committee emdatabank.org www.facebook.com/emdatabank3dem

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Question regarding uploading 2Fo-Fc map into KiNG
by Natalia Ketaren 07 Oct '15

07 Oct '15

Hello All, I have a question regarding the KiNG program: I used MolProbity to assess the quality of my model which revealed some poorly fitted residues in my structure. I want to correct these residues using KiNG but am having problems uploading the electron density map. Does the program not accept .mtz maps generated by coot? Do I have to convert the map into another file format? If so, would you be able to suggest a program for me with which to do this? Any help would be greatly appreciated! Kind regards, Natalia _____________________________ Natalia E. Ketaren, PhD Postdoctoral Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: (212) 327-8136 Fax: (212) 327-7193 Natalia.Ketaren(a)rockefeller.edu<mailto:[email protected]> website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/

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