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AUC2019. Registrations still open. Graduate and Postdoctoral scholarship awards available.
by Renwick Dobson 03 Jul '19

03 Jul '19

Dear Structural biology community, AUC2019<https://auc2019.uleth.ca/>, the 24th AUC Workshop and Symposium, will be held at the University of Canterbury, Christchurch (New Zealand) from 24-29 August 2019. 1) Registrations are now open and details can be found at this website: https://auc2019.uleth.ca/. Early Bird Registrations have been extended to the 15th July. 2) Beckman Coulter Life Sciences is generously offering one scholarship to a Graduate student and one to a Postdoctoral fellow to attend AUC2019 in Christchurch, New Zealand. Awardees will have their transportation (including airfare) and registration to the symposium and workshops covered (to a value of $1500USD). In addition, awardees will give a short talk in the symposium on their research. If you are interested, please submit the following to Ren Dobson (renwick.dobson(a)canterbury.ac.nz<mailto:[email protected]>) by the 18th July: i) a 400 word summary on how AUC has been used in your research, or alternatively, how you intend to use AUC during your research. (in pdf format) ii) A CV (in pdf format) iii) a scientific abstract for the talk. A template for the abstract is here: https://www.dropbox.com/s/sccrqoyp9wo7alm/NZ.AUC2019_AUC_SampleAbstract_for…. (submit in pdf format) Note, deadline for the Beckman Coulter Scholarships is the 18th July. The winners will be announced by the 31st July. 3) As the scientific program<https://auc2019.uleth.ca/symposium.php> for AUC2019 emerges, events will be uploaded to the website. We strongly encourage you to submit abstracts for talks and posters<https://auc2019.uleth.ca/abstracts.php>. 4) The format of the event is a 2-3 day workshop<https://auc2019.uleth.ca/workshops.php> offering parallel, hands-on training in experimental design and the latest AUC data analysis software from the world experts in this area followed by a 2 day research symposium on AUC and complementary approaches: methodological development, combination with orthogonal techniques (SAXS, SANS, SPR, MST, SEC-MALLS etc), application in biosciences and material sciences. 5) The meeting is also timed such that delegates can also attend the Biomolecular interactions and Engineering Symposium<https://www.queenstownresearchweek.org/bio-interactions/>, which is part of the Queenstown Molecular Biology Conference (this is in Queenstown, NZ), although note that this is a separate conference. 6) Lastly, The European Biophysics Journal has kindly agreed to run a special issue to celebrate the research presented at AUC2019. Therefore, we invite those who wish to extend their talks to a journal publication to consider contributing original research articles to this issue. Please indicate your interest for inclusion in this volume below. Deadline for registration of a contribution is August 30 2019. We look forward to welcoming you to Christchurch, New Zealand next Spring(-ish)! Ren Dobson, Chair AUC2019 On behalf of the AUC2019 Scientific Organising Committee ---- Prof. Ren Dobson Co-Director, Biomolecular Interaction Centre (BIC) http://www.bic.canterbury.ac.nz/ School of Biological Sciences | Te Kura Pūtaiao Koiora University of Canterbury | Te Whare Wānanga o Waitaha Private Bag 4800 Christchurch | Ōtautahi New Zealand | Aotearoa E: renwick.dobson(a)canterbury.ac.nz<mailto:[email protected]> T: ++64 (03) 369-5145 x 95145 F: ++64 (03) 364-2590 W: http://dobsonlab.org/

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intensity merging statistics for wwpdb deposition
by wtempel 03 Jul '19

03 Jul '19

Dear PHENIX users, how does one add merging statistics to PHENIX mmcif coordinates for deposition, assuming availability of AIMLESS logs and pre-merge intensities? Is this functionality implemented in PHENIX or CCTBX? Thanks. Wolfram Tempel

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r_work and r_free from an .mtz file containing Fobs and Fcalc
by Andre LB Ambrosio 01 Jul '19

01 Jul '19

Dear colleagues, Can Phenix calculate r_work and r_free from a .mtz file containing FP and FC_ALL (from PDB_REDO), without inputing the matching .pdb file? Many thanks in advance, -- Andre LB Ambrosio

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6th International Symposium on Diffraction Structural Biology: First Announcement
by Leighton Coates 01 Jul '19

01 Jul '19

Dear Colleague You are invited to the 6th International Symposium on Diffraction Structural Biology which will take place at the University of Osaka in Japan. Start Date: 17th Oct 2019 End Date: 20th Oct 2019 URL: https://isdsb2019.symposium-hp.jp/ The 6th International Symposium on Diffraction Structural Biology (ISDSB2019) is an international symposium organized by the Japan Society for the Promotion of Science, University-Industry Research Cooperative Research Committee, 169th Committee on Structural Biology using Diffraction Techniques. This symposium is positioned as an interface between academic researchers and industry researchers, as well as an interface between diffraction techniques and other related techniques in the field of structural biology. Symposium topics will include Macromolecular crystallography, CryoEM, software and databases, and drug discovery, registration and abstract submission for the symposium is now open and costs 25,000 Japanese yen for academics. A list of confirmed speakers for the symposium is currently being finalized; this will be posted on the symposium website within the next few days. Contact: Atsushi Nakagawa (Osaka University) Email: isdsb2019(a)gmail.com URL: https://isdsb2019.symposium-hp.jp/

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Mandatory PDBx/mmCIF format for crystallographic PDB depositions
by John Berrisford 01 Jul '19

01 Jul '19

>From today, July 1st 2019, submission of PDBx/mmCIF format files for crystallographic depositions to the PDB is mandatory. Refmac, Phenix.refine, and Buster programs can now output PDBx/mmCIF formatted files. For users of other structure determination/refinement software packages, the wwPDB provides stand-alone and web-based tools to convert legacy PDB format files into PDBx/mmCIF format: pdb_extract <http://pdb-extract.wwpdb.org/> and MAXIT <http://sw-tools.rcsb.org/apps/MAXIT/index.html> . More information on outputting and preparing PDBx/mmCIF format files for deposition can be found on the wwPDB website <https://www.wwpdb.org/deposition/preparing-pdbx-mmcif-files> . For more information, view the full news release at the wwPDB website <https://www.wwpdb.org/news/news?year=2019#5d17c1ceea7d0653b99c87e2> or contact the wwPDB on deposit-help(a)mail.wwpdb.org <mailto:[email protected]> . Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 <http://www.pdbe.org/> http://www.pdbe.org <http://www.facebook.com/proteindatabank> http://www.facebook.com/proteindatabank <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

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PEG as a polymer
by Felix Cat 29 Jun '19

29 Jun '19

Hi all, I'm working on a structure where I see extensive interaction of the protein with PEG (polyethylene glycol). The largest PEGs I can find in structures in the PDB with a quick search are around 12 EDO subunits long, and they're called "dodecaethanediol" or the like. I am seeing at least 20. Currently, I've built the PEG as a giant, single ligand, and generated a viable cif file for it using eLBOW with a SMILES string (very simple for PEG, you can imagine). I'm wondering if I might rather be able to handle it as a polymer of EDO subunits. I started to dig into that but got lost pretty quickly. I can't figure out how to create an automatically link-able EDO molecule, all with proper geometry, and I don't want to have to tell phenix.refine about 19+ custom linkages every time. (I've had to do that with N-linked acetylglucosamine moieties in the past.) Nate NUNC

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Real space refinement with helical symmetry
by Yangqi Gu 29 Jun '19

29 Jun '19

Hi all, I am trying to do a real space refinement with phenix and my map is a filament and I have monomer model and I would like to refine against my filament map. I am wondering how to impose the helical symmetry in this case? (I have a pseudo filament model by copying multiple subunits and aligned in Chimera using "fit in map"). Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

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CaBLAM fixing and interpretation in comprehensive validation for cryo-EM
by Ahmad Khalifa 28 Jun '19

28 Jun '19

Hello, I would appreciate some insights on how to interpret the validation results under the CaBLAM tab and how to use it to fix my structure in Coot? What are the CaBLAM score, the Ca geometry score, the helix score and the 3-10 score? How to use the information under the secondary structure tab? In my protein for example, I see a lot of "try beta sheets", should I try to refine that segment using beta sheets restraints? Best regards.

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(no subject)
by Pu Qian 28 Jun '19

28 Jun '19

Hi All I have a problem to do refinement for one of our cryo-em model caused by ligand of spirilloxanthin (wwPDB code CRT). I'm using phenix cryo-EM real-space refinement for one of my cryo-em models which contains a ligand called spirilloxanthin, a very common carotenoid molecule found in nature. Its code is CRT which can be found in wwPDB ligand dictionary and in COOT. However, when I run real-space refinement, I got a error message caused by this ligand "Fatal problem interpreting model file: Number of atoms with unknot non bonded type symbols: xxx please edit the model file to resolve the problem and /or supply a cis file with matching restrain definitions, along with apply_cif_modification and apply-cis-link parameter definitions if necessary". I checked my pdb file. All atom names and order are exactly same as that in wwPDB. I also try to insert it into map using COOT monomer find method. It does not work as well. It seems to me that Phenix can not recognise this ligand, CRT spirilloxanthin. Does anyone have an idea of how to deal with this issue. Or is it OK if I add CRT.cif into upload window of Phenix for refinement? Any suggestion is greatly appreciated. The version of Phenix I am using is Mac version recently downloaded from Phenix website. Best regards

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Position Opening: Synchrotron Macromolecular Crystallographer @ IMCA-CAT
by Lisa J. Keefe 28 Jun '19

28 Jun '19

Dear Colleagues, POSITION: Synchrotron Macromolecular Crystallographer LOCATION: IMCA-CAT at the Advanced Photon Source (near Chicago, IL) The Industrial Macromolecular Crystallography Association - Collaborative Access Team (IMCA-CAT) and the Hauptman-Woodward Medical Research Institute (HWI) seek an inventive macromolecular crystallographer to join the IMCA-CAT team in accelerating pharmaceutical drug discovery through synchrotron-based structural biology research. As an employee of HWI, you will be based at the center of the team’s operations at the Advanced Photon Source (APS), Argonne National Laboratory, near Chicago, IL. This is an ideal position for a motivated scientist who is passionate about delivering strategic value, developing new technologies, and working in a high- powered, collaborative environment. DESCRIPTION: This is an exciting time to join IMCA-CAT. Underway this summer is the first of a two-phase upgrade that will significantly increase throughput and establish a strong foundation upon which to build capacity. The second phase upgrade, currently in design, will profoundly increase capacity and dramatically expand capability for challenging research projects. The successful candidate will be an integral part of these upgrade activities while maintaining flow of diffraction data for pharmaceutical research projects. The candidate will work closely with IMCA-CAT colleagues in an inclusive and respectful environment, and is expected to take initiative and contribute to the team effort. On any given day, you will do one or all of these things: • Contribute to drug discovery research efforts using a growing portfolio of synchrotron sources. • Enhance the structural biology programs for pharmaceutical structure-based drug design. • Provide experiment support for scientists from the structural biology community who conduct research using the IMCA-CAT synchrotron beamlines. • Ensure beamline instrumentation is operational and produces data of the highest quality. • Expand the experiment envelope of the beamline. • Establish efficient protocols for accelerating data acquisition while enhancing data security. • Develop automated methods for acquiring quality data from challenging samples. • Participate in highly collaborative working groups. • Engage in the technical development of new strategies for ultra-high throughput. • Collaborate with staff on strategically-aligned research and development projects. • Communicate with researchers and present at meetings. • Conduct independent and/or collaborative research. DESIRED SKILLS and EXPERIENCE: • PhD in a relevant field. • Expertise in macromolecular crystallography. • Outstanding experimental skills. • Considerable mechanical skills. • Highly collaborative and team-oriented approach to conducting work and solving problems. • Excellent written and oral communication skills. • Deeply proactive approach to meeting and exceeding goals. • Ability to meet requirements for site access to Argonne National Laboratory. TO APPLY: Send an introductory email, cv, and contact information for three references to Lisa Keefe, IMCA-CAT Director and HWI Vice President of Advancing Therapeutics, at keefe(a)imca-cat.org. LEARN MORE: Visit our websites to learn more about IMCA-CAT (www.imca-cat.org) and HWI (www.hwi.buffalo.edu). HWI is an equal opportunity employer. Lisa J Keefe, PhD Director IMCA-CAT <http://www.imca-cat.org/> Industrial Macromolecular Crystallography Association - Collaborative Access Team 630.252.0544 • Sector 17 @ Advanced Photon Source, Argonne National Laboratory Vice President for Advancing Therapeutics Hauptman-Woodward Medical Research Institute <http://hwi.buffalo.edu/> Past-President American Crystallographic Association <http://www.amercrystalassn.org/> .

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