- phenixbb - phenix-online.org

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.

1 0

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>

2 1

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 >

1 0

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.

1 0

Positions at the NKI - Amsterdam
by Anastassis Perrakis 23 Oct '15

23 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

1 0

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 >

1 0

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

5 4

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

2 1

on cif file
by Smith Lee 19 Oct '15

19 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

1 0

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 >

2 2