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No NCS restrains in phenix.real_space_refine?
by Aaron Oakley 22 Jun '20

22 Jun '20

Am I correct in saying that phenix.real_space_refine does not (yet?) have NCS restraints (that I need for refining a molecule with broken symmetry)? With thanks, –å

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Water molecules whose existence is contingent on the alt conf of a side chain are deleted in refinement
by Dale Tronrud 18 Jun '20

18 Jun '20

Hi, I have a model with a Tyr side chain with two conformations. When it is in the A conformation three water molecules occupy the site of the B conformation. I have defined these water molecules to have the alt loc A (with no B versions) and set their occupancy equal to that of the A version of the Tyr. During refinement, using the GUI, these water molecules disappear during the "add/remove water" stage. My guess is they are running afoul of dist_sol_mol_min. I can't find where I can set this parameter to some, very small, value that will allow these waters to live and prosper. If this is my problem, how can I disable this check? Dale Tronrud

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PhD position (Denmark), Structural biology with a focus on sterol uptake mechanisms
by Bjørn Panyella Pedersen 15 Jun '20

15 Jun '20

Dear colleagues, Please pass this along any one who might be interested. Thanks! /Bjørn ============================================ STRUCTURAL AND FUNCTIONAL STUDIES of eukaryotic membrane proteins involved in sterol transport (http://pedersenlab.dk/source/phd_position_2020.pdf) A PhD position is available in membrane protein biochemistry and structural biology in the research group of Dr. Bjorn P Pedersen at the Department of Molecular Biology and Genetics, Aarhus University, Denmark. The group studies the structure-function relationship of membrane proteins involved in metabolite uptake, primarily sterol and sugar uptake, as well as their regulation from a structural perspective. The PhD project will involve expression, purification and structural/functional characterization of membrane proteins involved in sterol transport and homeostasis (Winkler et al. Cell 179 (2019)). Methods learned and used will be cryo-electron microscopy and X-ray crystallography, as well as various biochemical methods to elucidate function. The project is fully funded by the Danish Council for Independent Research, and will be based in the laboratory of Dr. Bjorn P. Pedersen (http://pedersenlab.dk). It would ideally suit an outstanding biochemistry graduate with a strong interest in structural biology. The candidate should have molecular biology, protein production and purification experience. Experience with membrane proteins or protein structure determination will be an advantage. Full training will be provided in all necessary areas of protein biochemistry and structural biology. Good English language skills are essential. Salary will be according to the collective agreement between the Danish Confederation of Professional Associations and the Danish State. The position will be filled as soon as a suitable candidate is identified. Applicant should send a CV, cover letter and names of two referees to Dr. Bjorn P Pedersen (bpp(a)mbg.au.dk). The city In Aarhus you have easy access to beautiful nature and an exciting culture and city life that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/locations/ for further details on the city and the university.

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Web server update
by Billy Poon 15 Jun '20

15 Jun '20

Hi everyone, The software running phenix-online.org has been updated. Please let us know if you experience any issues. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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ACA 70th Annual Meeting: August 2-7, 2020 - Abstract Deadline Monday 6/15!
by Lisa J. Keefe 12 Jun '20

12 Jun '20

<http://clicks.memberclicks-mail.net/ls/click?upn=RB8hRfLA-2BDSUW5jji7-2Bs5f…> The deadline to submit an abstract for an oral presentation is Monday, June 15, 2020! Submit An Abstract Today! <http://clicks.memberclicks-mail.net/ls/click?upn=RB8hRfLA-2BDSUW5jji7-2Bs5f…> “Training the Next Generation” <http://clicks.memberclicks-mail.net/ls/click?upn=RB8hRfLA-2BDSUW5jji7-2Bs5f…> 1.1.4 & 1.2.2 Microcrystal Electron Diffraction (MicroED) – Small Molecule & Macromolecules 1.2.3 Communicating Science to the Public 1.2.5 In situ / operando: From Synthesis to Devices 1.2.4 Advances in Fiber Diffraction 2.1.4 Frontiers in SAS 2.3.1 Would You Publish This? 1.2.1 Remote Access Facilities: What, Where & How? 2.1.2 Advances in Software Methods and Tools for Cryo-EM 3.2.3 Structural Contributions to SARS-CoV2 and the COVID-19 Pandemic T1&2 Structural Science: New Ways to Teach the Next Generation 4.1.2 Structural Dynamics I. Protein Collective Motions Studied by X-ray Scattering and Diffraction 4.2.4 Physics and Chemistry of Matter Under Extreme Conditions 3.1.1 CryoEM in Pharma: Structure-based drug design beyond X-ray crystallography 4.2.2 Structural Dynamics II. Conformational Ensembles of Proteins Studied by Cryo-EM and X-ray Scattering 2.2.3 & 4.2.3 General Interest 3.1.4 & 3.2.4 Cool Structures: Important Science from Small Molecules 4.1.1 Methods and Tools for Crystallography and Cryo-EM Sample Preparation 3.2.3 Hot Structures *** There is no fee to submit an abstract, but you must be an ACA member to submit an abstract or attend the meeting. Join or renew today! <http://clicks.memberclicks-mail.net/ls/click?upn=RB8hRfLA-2BDSUW5jji7-2Bs5f…> For more information and to register to attend the meeting, visit our conference website at www.acameeting.com <http://clicks.memberclicks-mail.net/ls/click?upn=RB8hRfLA-2BDSUW5jji7-2Bs5f…>. -The American Crystallographic Association- <http://clicks.memberclicks-mail.net/ls/click?upn=RB8hRfLA-2BDSUW5jji7-2Bs5f…>

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phenix eLBOW and phosphorous stereochemistry
by Xavier Brazzolotto 11 Jun '20

11 Jun '20

Dear all, I use phenix.elbow in order to generate mol2 files that will then be used in a docking process through autodock/vina. I am facing a strange issue. While using a SMILES string bearing stereochemistry at a desired phosphorous atom as eLBOW input file, the correct stereochemistry is not respected in the output files. While giving PR or PR compound, I always end up with the very same enantiomer… Maybe eLBOW does not handle the phosphorous specific stereochemistry ? Many thanks Xavier Brazzolotto, PhD

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SSBOND for protein-ligand
by Wei Wang 09 Jun '20

09 Jun '20

Dear all, I’m seeking help for establishing disulfide bond between protein and ligand. I used phenix.readyset to prepare the model for refinement then used phenix.elbow to generate the cif for ligand. After refinement, the sulfur from ligand, which was meant to be forming disulfide bond, is linked to the adjacent CYS by dashed line. I do see the LINK record in refined pdb. I tried manually add SSBOND record line in the pdb, following format instructions on wwpdb, but didn’t succeed. Thus I’m here looking for help on how to properly introduce disulfide bond between a ligand and cysteine. Some further explanation: When I display the readyset output in Pymol, the disulfide bond seems to be correctly recognized. I guess it’s because the sulfur atoms are within the detectable distance for a SSBOND. When I opened the same pdb in Coot, the disulfide bond is not present. I noticed a similar situation in PDB:6O9V, where the ligand M1M (chain B and resseq 401) was refined with LINK record but not SSBOND. (Sorry if this is a repeat message: previous message was put on hold because attachment pic size was too big.) Regards, Wei

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Phasing@Home event
by Claudia Millán Nebot 05 Jun '20

05 Jun '20

Dear PhenixBb community, We are glad to announce the first Phasing@Home event, an online meeting devoted to presenting XDS, ARCIMBOLDO, Phaser and SHELX software and their use in challenging phasing cases. Confirmed speakers and members of the teams: Institut de Biologia Molecular de Barcelona (IBMB-CSIC): Isabel Usón, Claudia Millán, Ana Medina, Iracema Caballero, Elisabet Jimenez, Albert Castellví, Giovanna Petrillo, Josep Triviño Cambridge Institute for Medical Research (CIMR): Randy Read, Airlie McCoy, Rob Oeffner, Kaushik Hatti, Massimo Sammito, Tristan Croll University of Konstanz: Kay Diederichs University of Goettingen: George Sheldrick Instituto de Biociencias, Universidade Estadual Paulista (UNESP): Rafael Borges The full schedule can be found under: http://chango.ibmb.csic.es/phasingathome The meeting will hosted via Zoom and is free of charge but you will need to pre-register here: https://www.eventbrite.co.uk/e/phasinghome-tickets-107673520398 The event will be held online on the 13th and 14th of July. Talks will be short and focused on covering the advanced usage of the software, so participants are expected to be familiar with the basics already or to browse some basic material provided by us in advance. Interaction among speakers and participants will be through a Discord (https://discord.com/) server. Please note that this event is limited to 25 external participants and provided they meet the requirements of presenting some challenging dataset, the acceptance upon registration will be on a first-come, first-served basis. With best wishes, ---------------------------------------------------------------------------------------- Claudia Millán (cmncri(a)ibmb.csic.es) Crystallographic Methods Group http://chango.ibmb.csic.es Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain LinkedIn: es.linkedin.com/in/claudiamillan/ <http://es.linkedin.com/pub/claudia-mill%C3%A1n/60/a76/821/> ResearchGate: https://www.researchgate.net/profile/Claudia_Millan?ev=hdr_xprf Twitter: https://twitter.com/cheshireminima and Massimo Sammito

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Amber module in phenix on Ubuntu 18.04
by Guenter Fritz 04 Jun '20

04 Jun '20

Dear all, dear Nigel, I cannot get the Amber and AFITT menu bars in the phenix.refine GUI on a Ubuntu (Xubuntu 18.04) box. I set Preferences "Enable alpha-test programs and features" (works on my Mac 10.14.6 and SciLinux6 box ). Moreover, on the Xubuntu machine: when I start the phenix.refine GUI (phenix version 1.18.2-3874) I see the following error message in the terminal running phenix: //$ phenix// /Could not import the compiled Python-sander interface. Make sure you have the Python development libraries installed and that you have sourced amber.sh or amber.csh / //------------------------// python 3.7 is installed and python development tools :/ / /------------------------ / /$ python -V // //Python 3.7.6 / /$ sudo apt list -a python3.7-dev // //Listing... Done // //python3.7-dev/bionic-updates,now 3.7.5-2~18.04 amd64 [installed] // //python3.7-dev/bionic-security 3.7.3-2~18.04.1 amd64 // //python3.7-dev/bionic 3.7.0~b3-1 amd64 / /------------------------/ Any idea what is going wrong? Thanks a lot and best regards, Guenter

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Post-doctoral position in Neutron/X-ray crystallography at the Institut Laue Langevin (Grenoble, FR)
by Nicolas Coquelle 03 Jun '20

03 Jun '20

Dear all, The Large Scale Structure group of the Institut Laue Langevin (Grenoble, FR), in collaboration with the group of Elspeth Garman (Oxford, UK) has an open position for a post-doctoral fellow in neutron/X-ray crystallography to study radiation-damage. Please see the description below and contact me (coquelleni(a)ill.fr <mailto:[email protected]>) for further information. Best regards, Nicolas Coquelle.

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