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mr_rosetta build test
by Wei Wang 18 Jul '20

18 Jul '20

Dear all, I would like to ask a question about the testing of mr_rosetta build. Is the “phenix_regression.wizards.test_command_line_rosetta_quick" still available? I checked my early build on Mac it is there, but that build was ~3 years ago. However on a recent build on Ubuntu 18.04 the option is not available (I ran the rosetta.run_tests and it’s ok though). Regards, Wei

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occupancy_sum_constraints
by Petros Giastas 16 Jul '20

16 Jul '20

Dear all, I have a metal compound interacting with a protein and I am facing the following problem. Initially, the metal is equatorially complexed with chlorides, which are progressively exchanged by water molecules. This hydrolysis is clear from our spectroscopic analysis, but also from the anomalous maps, which show weaker peaks for the most exposed chlorides. The question regarding phenix.refine is: How can I refine the occupancies of the alternative species (chlorides and water molecules) and to constrain their sum into the occupancy of the metal, which is also under refinement? I cannot find the proper selection syntax to deal with this situation. Can you help me on that? Thank you in advance. Petros P.S. I remember I could treat this kind of problem with shelxl but it has been a lot of time since I last used shelxl for high resolution protein refinement and I would not like to go back.

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PhD position (Denmark), Structural biology with a focus on sterol uptake mechanisms
by Bjørn Panyella Pedersen 13 Jul '20

13 Jul '20

Dear colleagues, We have a open PhD position my my group. Please pass along to anyone who might be interested. Thanks! Deadline is July 31st. /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. Deadline is July 31st. Applicant should send a CV, cover letter and names of two referees to Dr. Bjorn P Pedersen (bpp(a)mbg.au.dk).

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phenix writing files with wrong job number
by Green, Todd Jason 09 Jul '20

09 Jul '20

Hello All- Phenix has started to write files from each job with incorrect job number notation. It puts them into the correct directory (ie. with correct job number, ex. Refine_23) but with file names having wrong job number (ie. where they are job number - 1, ex. protein_refine_22.pdb). This causes issues with the gui. I can edit the names post run, but is there a permanent fix. Just start a new project? Probably upgrade to the new version is the first choice. FYI I'm running 1.17.1-3660-000 on a macbook. Seems to have just started spontaneously. Thanks for the help- Todd

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The 5'end guanosine triphosphate is not linked to the rest of RNA model by Phenix refine
by Zixian Li 08 Jul '20

08 Jul '20

Dear Phenix Community, I'm at beginner level of using Phenix. I have difficulty to refine a protein-RNA complex in Phenix. I refined the protein model without RNA first, then I built the RNA model into the difference density map in Coot through Calculate>Other Modelling Tools>Ideal DNA/RNA, where I input the sequence and fit nucleotides into the density. At the 5' end it's guanosine triphosphate (GTP) but the modeler tool in Coot only generates nucleoside monophosphate. So I built the RNA model from the second nucleotide at 5' end downstream until where RNA density was too poor to model. I did the real space refine zone in Coot to fit this main part of the RNA into its density the best possibly. For the GTP at 5' end, I realized there is GTP.cif restraint file in Phenix monomer library. So I obtained an arbitrary pdb file for GTP using eLBOW and corrected atom names matching the definition in GTP.cif file. Then I can also fit GTP into the RNA density at 5' end using real space refine zone in Coot. Now I have a broken RNA model with GTP unlinked to the ribose-phosphate backbone. For Phenix refinement, I supplied a cif_link_GTP-G.params file to define the linkage for the two RNA chains in the complex: refinement.pdb_interpretation { apply_cif_link { data_link = p residue_selection_1 = chain C and resname GTP and resid 1 residue_selection_2 = chain C and resname G and resid 2 } apply_cif_link { data_link = p residue_selection_1 = chain D and resname GTP and resid 1 residue_selection_2 = chain D and resname G and resid 2 } } After refinement, I noticed O3' of GTP appears connected to P of the following nucleotide G in the refined model in Coot. However, if I do the real space refine zone in Coot, the linkage becomes broken, i.e., I cannot refine the RNA model as a whole: Coot only allows separate real space refine for GTP and the rest. It seems Coot still cannot recognize GTP and the rest as one body. In the refinement settings there is a button for Automatic linking options. Interestingly, I noticed if I leave the automatic covalent linking as default, Phenix writes Link records in the output pdb after refinement. But it also links one of the protein residues to the GTP in chain D. In order to avoid the unwanted intermolecular linkage, I clicked Link none for Automatic linking options, then there is no any link records written in the output pdb despite of the defined linkage in cif_link_GTP-G.params file. So it seems for me Phenix ignores the input cif_link_GTP-G.params file, it writes Link records only if the Automatic linking option is activated. I worried whether it could be due to the syntax of the cif_link_GTP-G.params file. So I tried the following syntax in two separate files, the same issue was observed. cif_link_GTP-G_chC.params refinement.pdb_interpretation.apply_cif_link { data_link = p residue_selection_1 = chain C and resname GTP and resid 1 residue_selection_2 = chain C and resname G and resid 2 } cif_link_GTP-G_chD.params refinement.pdb_interpretation.apply_cif_link { data_link = p residue_selection_1 = chain D and resname GTP and resid 1 residue_selection_2 = chain D and resname G and resid 2 } I also need to point out that p linkage is pre-defined in the list of links (mon_lib_list.cif) in Phenix monomer library. I apologize for this long explanation of the problem. I hope it is clear. I really appreciate your advice in advance. Sincerely, Zixian Li

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Heteroatoms addition to crystal structures
by Shirin Akbar 06 Jul '20

06 Jul '20

Dear all, I am using the phenix.real_space_refine program for refinement of crystal structure in cryo-EM map (ribosome map, 3.4 A resolution). Prior to real_space_refinement I had removed all the heteroatoms. What is the correct way to add the cations (eg. Mg2+ ions) to the structure and how do I do it? Can anyone kindly suggest.. Thanks & Regards Shirin -- *Shirin Akbar*

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real-space refinement resolution
by Alexei Gorelik 30 Jun '20

30 Jun '20

Hi, When refining a model against a density-modified cryo-EM map, should one use the resolution of the original or modified map? Thanks

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Refining cytochrome structure with hemes
by Yangqi Gu 30 Jun '20

30 Jun '20

Dear Phenix developers. I have a simple question regarding the real space refinement. I am working on a cytochrome structure and I would like to know how to refine the model with hemes present against the map? Also, how do I create vinyl bonds at my cysteine positions to connect the hemes? More ideally, could I refine the heme geometry as well? Thank you in advance! Best, Yangqi

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CryoEM Post-Doctoral Position
by Hasan, Syed Saif 25 Jun '20

25 Jun '20

Interested in exploring the world of molecular espionage? Want to find out how viruses hitchhike between organelles during assembly? Join my lab as a post-doctoral researcher to decipher the secret life of epidemic causing viruses at the atomic scale. We use high-resolution single particle cryoEM and X-ray crystallography to investigate how viruses such as Dengue, SARS-CoV-2, and pox viruses take over host membranes during intra-cellular progeny assembly. We are located in Rockville MD in the Institute for Bioscience and Biotechnology Research (IBBR; https://www.ibbr.umd.edu/profiles/s-saif-hasan), which is 20 miles north-west of Washington DC. In IBBR, you will have in-house access to a 200 keV Talos Arctica with a Falcon 3EC DED and a 200 keV Glacios with a K3 DED and a Volta Phase Plate (VPP). We have off-site access to a Titan Krios microscope equipped with DED and VPP. For X-ray crystallography, we have access to a Mosquito crystallization robot. Data collection is usually performed at synchrotrons. Our research is highly collaborative and is supported by wonderful colleagues who help us out with their expertise in NMR spectroscopy, lipidomics, HDX-MS, MD simulations, computer assisted drug design, and cellular imaging. If you are interested, send me your CV. Lets talk. ************************************************************************************************ The University of Maryland, Baltimore is an Equal Opportunity, Affirmative Action employer. Minorities, women, individuals with disabilities and protected veterans are encouraged to apply. ************************************************************************************************ Saif S. Saif Hasan, PhD Assistant Professor Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine 108 N. Greene Street, Baltimore MD 21201 https://www.medschool.umaryland.edu/profiles/Hasan-S-Saif-Hasan-Syed-Saif/ Associate Member Program in Oncology, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center (UMGCCC) 22 S. Greene Street, Baltimore MD 21201 Office and Laboratory Address: Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research (IBBR) 9600 Gudelsky Drive, Rockville MD 20850 https://www.ibbr.umd.edu/profiles/s-saif-hasan Phone: 240-314-6396 Fax: 240-314-6225

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Energy minimization and explicit solvent model
by Andre LB Ambrosio 24 Jun '20

24 Jun '20

Dear colleagues, could you please suggest a computational tool to perform energy minimization of a crystal structure under explicit solvent conditions (i.e, types and concentrations of ions, pH)? I want to observe the solvent effects on the conformational space around a starting model, all-atom, while preserving its geometry (I guess it can be better expressed as relaxation). Thank you in advance. -- Andre LB Ambrosio

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Senior Scientist Position at AbbVie
by Jain, Rinku 24 Jun '20

24 Jun '20

Hi Everyone, I would like to draw your attention to the following job opportunity at AbbVie: Senior Scientist I, Protein X-ray Crystallography https://careers.abbvie.com/abbvie/jobs/2004610?lang=en-us&previousLocale=en… The Protein Crystallography Group at AbbVie (Illinois, USA) is seeking a highly motivated scientist to join our Structure-Based Drug Discovery team. The ideal candidate should have extensive hands-on experience in modern X-ray Crystallography techniques and computational methods of molecular structure analysis. As part of multidisciplinary teams, the Scientist will utilize fragment-based strategies to identify ligands and provide insight to advance drug discovery targets through structure-based design. The successful candidate will contribute to drug discovery projects across the portfolio of AbbVie interests that also include therapeutic antibodies and novel biologics. AbbVie (NYSE:ABBV) is a global, research-driven biopharmaceutical company committed to developing innovative advanced therapies for some of the world's most complex and critical conditions. The company's mission is to use its expertise, dedicated people and unique approach to innovation to markedly improve treatments across four primary therapeutic areas: immunology, oncology, virology and neuroscience. In more than 75 countries, AbbVie employees are working every day to advance health solutions for people around the world. To learn more about AbbVie, please visit: https://www.abbvie.com/ Best, Rinku --------------------------------------------------------------------------------------------------------------------------------------------------- Rinku Jain, Ph.D. Senior Scientist II, Structural Biology [cid:[email protected]] I AbbVie, Inc. 1N. Waukegan Road, AP10-LL North Chicago, IL 60064-6098 EMAIL rinku.jain(a)abbvie.com<mailto:[email protected]>

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13th CCP4/APS Crystallographic School in the US
by Xu, Qingping 24 Jun '20

24 Jun '20

Dear Colleagues, We are pleased to announce the 13th annual CCP4/APS crystallographic school “From data collection to structure refinement and beyond” will be held on June 15-22, 2020 at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2020/index.php. Dates: June 15 through 22, 2020 Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: data collection workshop and crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, contact info and other details can be found at the School website. Applicants: Graduate students, postdoctoral researchers and early-career faculty, along with commercial/industrial researchers are encouraged to apply. Only about 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 1th, 2020. To apply, visit https://www.ccp4.ac.uk/schools/APS-2020/application.php<https://www.ccp4.ac.uk/schools/APS-2019/application.php>. Fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for industrial researchers. A valid credit card is required for registration, however, it will be charged only for students selected to participate. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, Garib and Qingping

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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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Imposing bond restraints across the asymmetric unit
by Brandon J Anson 28 May '20

28 May '20

Hello, I have an unusual problem in which my enzyme (a dimer) is covalently bound to its own C-terminus and so is daisy-chained across the crystal lattice. In the past, I have encountered and fixed this problem by extracting the covalent part of the molecule and re-phasing using that as the molecular replacement model. In this case, I am not able to due so. When I input the restraints, it either crashes refine or attempts to impose them on the corresponding residues within the ASU (understandable) but they are quite distal and this leads to "interesting" refinement results. Is there a good way of making phenix.refine do what I want? Or perhaps a workaround that I haven't considered yet? Best Regards, Brandon

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Refinement problem in phenix
by Muhammad Bashir Khan 23 May '20

23 May '20

Hi there; I find some unknown density in my map, where I put SO4 and in some UNX. I merged and save all in one PDB. I run ReadySet to make cif. file, but refinement still not working. Can anybody explain what else I should provide? Thanks in advance Bashir -- ------------------------------------------------------ Muhammad Bashir Khan, Ph.D. Research Associate Department of Biochemistry Medical Science Bldg. Lab 3-27 University of Alberta Edmonton AB, T6G 2H7 Phone: 780-492-4577- e-mail: mbk(a)ualberta.ca <cbrooks1(a)ualberta.ca>

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symmetry conflicts
by Daniel Larsson 22 May '20

22 May '20

I want to report an annoying bug in version 1.18.2-3874. My real_space_refine job ended with an error at the validation step saying Crystal symmetry mismatch between different files. This was when refining a PDB structure (first processed using ready_set) in a cryo-EM map. The “Ignore symmetry conflicts” checkbox was checked. The expected output files were generated, but no validation report was generated. Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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byron bender
by Taufiq El-Mokdad 22 May '20

22 May '20

Hi all, I am a student from Halle in Germany. I really want to try out doing a wire model for proteins with the Byron Bending machine, yet I couldn’t find out where to get one and the Charles Supper Company discontinued selling these devices. I was recommended asking here for help. Is there anybody still having one of these devices in their labs or having one starting to rust in a box in the attic? I would be really statisfied trying out making some wire protein models with it. If someone would be willing to give such a machine and I would of course pay the shipping costs I would be happy to hear about. I would also be grateful if someone could give me a tip where I could still ask? Thanks.. All the best Taufiq

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Alternative conformation on special position occupancy wrong
by Kaiser, Jens T. 21 May '20

21 May '20

Hi, We have a case of a cofactor with 222 symmetry in two states on a special position ( 2-fold). When modelling one state, Phenix correctly restrains the occupancy to 0.5. When putting state 2 in alternative conformation group B, the occupancy of altconf A and B is restrained to 1.0, instead of 0.5; it seems like it does not recognize that the alternative conformations are on a special position. Cheers, Jens Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Phenix version 1.18 released
by Paul Adams 20 May '20

20 May '20

The Phenix developers are pleased to announce that version 1.18 of Phenix is now available (build 1.18.2-3874). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Please note that this recent publication should now be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Highlights for the 1.18.2 version of Phenix: 1.18.2 Changes - Fix weighting for iron sulfur clusters 1.18.1 Changes - General bug fixes 1.18 Changes - Amber - Automatic creation of Amber files in phenix.refine GUI - Added AmberPrep GUI - Restraints - Engh & Huber restraints (2001) for cis-peptides now implemented - Restraints added for FeS - Metal coordination library is default to Zn+2 and FeS clusters - Rama-Z: New global Ramachandran score for identifying protein structures with unlikely stereochemistry in CLI (phenix.rama_z, mmtbx.rama_z) and GUI (validation reports). - Density modification for cryo-EM - Includes model-based density modification with automatic model generation - Optimized defaults and additional documentation - Real-space refinement - Hydrogen atoms no longer included in map target function, which improves fit. - Add NQH flip option (enabled by default) - Other - New tool for ordered solvent picking in cryo-EM maps (phenix.douse) - New map and model superposition tool (phenix.match_maps) - New FindProgram to find any Phenix program with a text search - Project details now has a button for opening the README file for tutorials For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this new publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleydawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Generating a polder map using coordinates
by Petr Kolenko 20 May '20

20 May '20

Dear colleagues, Is there a way to calculate the polder map in a selected box using coordinates instead of atom selection as shown in the "Generating a polder map with the compute_box option" website? Best regards, Petr

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Solving a protein - ligand structure
by Tom Vanmarcke 20 May '20

20 May '20

Dear, We are trying to solve a protein structure that contains a ligand (polyoxometalate). We found the ligand in the electron density but through the middle of the ligand goes a 2 fold axis. For this reason, we placed the occupendency of the ligand on 0.50. When we try to refine the structure using phenix.refine, the ligand breaks down even when adding a cif restrain file. The cif restrain file contains information about atoms, angles and bond lengths. Is there a way to fix this problem? Greetings Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Is there a way to evaluate batch pdb models with Malprobity in phenix?
by Jing Liu 19 May '20

19 May '20

Hi, I had generate a batch of pdb models (40-100) in rosetta and am wondering whether there is a way to evaluate these models in batch with Molprobity. For example, can I use phenix command line to do it and how? Or should I download the Molprobity and do it on my local computer? Really appreciate if anyone can share their experience. Jing Liu, PhD Ted Jardetzky lab Department of Structural Biology Stanford University

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Phenix 1.18 and rotamer outliers
by Xavier Brazzolotto 18 May '20

18 May '20

I’ve installed the latest stable Phenix version (1.18). I’ve noticed a clear difference in the final statistics (MOLprobity) compared to the previous version (1.17). A bit more of Rama outliers and the most noticeable in the Rotamer outlier score. Is there any reason that could explain such behaviour ? I am using Phenix under MacOS. Xavier Brazzolotto, PhD xavier.brazzolotto(a)chemdef.fr Département de Toxicologie et Risques Chimiques Unité Neurotoxiques Institut de Recherche Biomédicale des Armées 1 Place du Général Valérie André, BP 73 91223 Brétigny sur Orge France Phone +33 (0) 1 78 65 14 00 Alt Phone +33 (0) 4 57 42 87 19 Cell +33 (0) 6 58 36 39 09 The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. This is not an official email address of the French Ministry of the Armed Forces. It does not allow diffusion of protected informations and does not necessarily complies to the ministry cyber security policy.

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unit cell dimesions
by Thomas, Leonard M. 13 May '20

13 May '20

Hello All, I have run into something that has me a bit puzzled. When finishing up a structure we ended reprocessing the data to get nice statistics for deposition, I don’t want to get into that discussion. Upon reprocessing the unit cell dimensions shifted slightly, 0.05 A or so. The PDB file used had the unit cell from the original solution/refinement while the data set cell dimensions were different. I ran the newly processed reflection data set through the reflection editor in order to transfer the Rfree set. Now the really odd thing is that I ended up reprocessing a couple times and transferring over the Rfree set once more. The cell dimensions on the final reflection file is from not the original reflection file/PDB but one that was used with an intermediate cutoff between the two, it is not the cell dimensions in the input reflection either. Just for completeness the data were processed using XDS at SSRL. My question is where does phenix.refine pick up the unit cell dimensions and were does the reflection file editor pick them up? Best Regards Len Leonard Thomas, Ph.D. Macromolecular Crystallography Laboratory Oklahoma COBRE in Structural Biology Price Family Foundation Institute of Structural Biology University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 Office: (405)325-1126 lmthomas(a)ou.edu<mailto:[email protected]> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl

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install fail in linux
by 안우찬 12 May '20

12 May '20

Hi, I have a problem with install phenix-1.18.1-3865 in linux. My linux version is NAME="Red Hat Enterprise Linux Atomic Host" VERSION="7.4.0.4". The error massage is ============================================================================= Traceback (most recent call last): File "./bin/install.py", line 244, in <module> installer(sys.argv[1:]).install() File "/home01/x1959a02/phenix/phenix-installer-1.18.1-3865-intel-linux-2.6-x86_64-centos6/li b/libtbx/auto_build/install_distribution.py", line 190, in install self.check_directories() File "/home01/x1959a02/phenix/phenix-installer-1.18.1-3865-intel-linux-2.6-x86_64-centos6/li b/libtbx/auto_build/install_distribution.py", line 268, in check_directories os.makedirs(i) File "/usr/lib64/python2.7/os.py", line 157, in makedirs mkdir(name, mode) ============================================================================= Thanks in advance, Teddy Ahn

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How to compare between electron density maps?
by Murpholino Peligro 12 May '20

12 May '20

I want to compare electron density features of map A from protein A and map B from protein B... Because each map has a different rmsd level... ...what is the best way to compare electron density between maps? Is there a way to normalize maps or something like that? Thanks

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Is there a way to search the phenixbb mailing list archive?
by Murpholino Peligro 11 May '20

11 May '20

With the ccp4bb at https://www.jiscmail.ac.uk/cgi-bin/webadmin I can search for a term in the archive. Is there something similar in the phenixbb? Thanks Or... is there a way to wget all the gz files?

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Online Course on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 11 May '20

11 May '20

ORNL Online Course on Neutron Scattering Applications in Structural Biology (https://conference.sns.gov/event/217/) June 1 - June 5, 2020 2:00 pm - 5:30 pm EST Registration (free) is now open and will close May 17, 2020. This online course is designed for graduate students, post-doctoral researchers and faculty with knowledge of structure and function of biological macromolecules but with limited to no experience with neutron sciences. The course will cover the basics of deuterium labeling, small angle neutron scattering, neutron reflectometry, neutron spectroscopy, neutron imaging and neutron crystallography. Instrumentation, sample preparation, data collection and processing will be introduced for each neutron technique.

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Boost 1.70 update for cctbx
by Billy Poon 09 May '20

09 May '20

Hi everyone, There is currently a pull request for cctbx that will update Boost to 1.70 ( https://github.com/cctbx/cctbx_project/pull/409). The update enables support for Python 3.7 and 3.8. The plan is to merge this next Friday, May 8, at 3 pm Pacific. After merging, developers should delete the build/lib/*boost* files and build/boost directory so that any remnants of the old Boost are removed and then rebuild. Let me know if you have any questions. 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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Phenix installation
by Sam Tang 06 May '20

06 May '20

Hi I am installing Phenix on a Fedora 30 station. It complains line 15: /usr/bin/python: No such file or directory. I have checked that there is python3.7.3 pre-loaded. So did I miss anything obvious...? Brs Sam

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Ligand refinement - geometry does not fit density
by Schulz, Eike-Christian 04 May '20

04 May '20

Dear all, I am refining a structure with a simple ligand in phenix 1.14. The ligand is present in 2 conformations at approx. equal occupancy. Refinement of the 2 conformations runs smoothly, but 2 problems occur 1. One of the ligand atoms is placed out of the electron density after refinement. The geometry file (via elbow) is present during refinement. The atom is not in an extreme position or clashes with anything else. 2. After refinement the ligand conformation cannot be changed in coot, although I import the cif dictionary. Any advise ? Best, Eike

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Phenix 1.18 RSR runtime
by Hannah Bridges 02 May '20

02 May '20

Dear Phenix developers, We have updated to phenix version 1.18-3845-000 and found that realspace refinement (5 cycles) with minimization global, local grid search and ADP is taking about 36 hours, compared to ~ 1hr in versions 1.17 and 1.16. The slow step is the local grid search which is taking >6 hours each cycle. We are very glad for the option to run the job detached, but I wondered if this sort of timing was expected for this version? Best wishes Hannah -- Dr Hannah Bridges Investigator Scientist MRC Mitochondrial Biology Unit The Keith Peters Building University of Cambridge Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY United Kingdom Telephone : 01223 252812

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off-topic; suggestions for 96head liquid handler
by Georg Mlynek 30 Apr '20

30 Apr '20

Dear Scientific community, we have lend over Viaflow96 liquid handler (used for pipetting 35-50 uL in 96 well crystallization plates) to our Covid -19 Diagnostics Initiative. As we believe that this story will be ongoing for some longer time I am looking for a new 96 head liquid handler. We are happy with the Viaflow and have two heads 10-300 uL; 0.5-12.5 uL. However one tip box (96 tips for the 10-300 uL) is about 4 €. This compares to ~1 € for the refilling racks we use for our single channel pipettes (It is said that boxes have to be more rigid, because of pressure during tip loading). Therefore if you have a 96 head liquid handler for volumes of 20-60 uL where cheap tips can be used (automation not necessary) please write me. Many thanks in advance, best regards, Georg.

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Computational Crystallography Newsletter (CCN) release and submissions
by Nigel Moriarty 28 Apr '20

28 Apr '20

Folks Recent world events have affected many things including the timely release of the CCN. Please consider this the Shelter-In-Place edition. Many of you will be involved in SARS-CoV-2 research and the CCN for July 2020 can be a vehicle for publishing the more community interest details. The deadline for submissions is 1 JUN 2020. 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, Molecular Biophysics and Integrated Bioimaging 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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Open postdoc positions in the Gonen lab
by Johan Hattne 26 Apr '20

26 Apr '20

Dear all; We would like to draw your attention to two HHMI-funded postdoc positions in the laboratory of Tamir Gonen at the University of California, Los Angeles. The first position concerns the biochemistry of membrane proteins, the second is focused on computational methods development. For further information, as well as application instructions, see the links below. Biochemistry https://hhmi-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.jobin… Programming https://hhmi-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.jobin… // Best wishes; Johan

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Two conformation of a ligand
by Muhammad Bashir Khan 22 Apr '20

22 Apr '20

Hi All; I have a structure where I believe that the ligand is bind in two conformations. In the Ligand Fit, it places only one even I select conformer 2. My other question is, Is there a way that I can use a reference PDB bound to the ligand in the Ligand Fit to help it placing my ligand. Thanks for your help in advance Bashir -- ------------------------------------------------------ Muhammad Bashir Khan, Ph.D. Research Associate Department of Biochemistry Medical Science Bldg. Lab 3-27 University of Alberta Edmonton AB, T6G 2H7 Phone: 780-492-4577- e-mail: mbk(a)ualberta.ca <cbrooks1(a)ualberta.ca>

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Problems displaying disulphide links
by Urvashi Sharma 21 Apr '20

21 Apr '20

Dear all, I have a problems displaying disulphide links in PyMoL and CCP4mg for a 2.3 angstrom crystal structure. I have tried both PyMoL and CCP4mg, these programs are not recognizing an important inter-domain disulphide bridge which seems to have no problems in "Coot". While other intra-domain disulphide links are fine. Can anyone suggest how to manually fix it? In addition, I have performed protein-protein docking using this crystal structure and have obtained nice convincing model. However, in this pose, which is being refined and energy minimized, none of the disulphide links are intact! Upon manual examination, I have noticed that the corresponding cysteine are 3.0-4.0 angstrom away. How should I correct this? Looking forward to your suggestions... With thanks and regards, Urvashi ---------------------------------------------------- Dr Urvashi Sharma, DBT-Ramalingaswamy faculty fellow JNU, New Delhi.

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Error log
by Viswanathan Chandrasekaran 16 Apr '20

16 Apr '20

Hi all, Other than resubmitting the job, is there a way to retrieve the contents of the Phenix error dialog box that appears at the end of a failed job? It is not present in the log file. Thanks, Vish

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iNEXT-Discovery: Access to facilities for structural biology research
by a.perrakis＠nki.nl 16 Apr '20

16 Apr '20

Dear all, While being in turbulent times, iNEXT-Discovery, the EC Horizon-2020 project offering access to facilities for structural biology (EM, NMR, X-rays and macromolecular biophysics), has officially started its operations. iNEXT-Discovery encourages applications for structural biology projects for ‘translational research projects’ in the areas of biomedicine, biotechnology, biomaterials and in the food sector, in particular from non-experts and for researchers from academia and industry. We are now happy to announce to the wider research community our new website with details about the project and where applications for access to the participating facilities can be submitted: https://inext-discovery.eu<https://inext-discovery.eu/> Regardless of current corona-measures external researchers are more than welcome to apply for access and we expect reviewing of incoming proposals to proceed as normal. However, please keep in mind that most facilities are currently not operational, and it is uncertain when they will open again to deliver access and to receive visitors. We will not be able to give a detailed overview about the status of all facilities, as the situation is changing almost daily. Having accepted applications in our access pipelines will help both our scheduling and yours. Our facilities can arrange experiments for approved user projects to be executed immediately after local policies allow. Please note that applications addressing SARS-CoV-2 or Covid-19 and mentioning this in the title will be funneled towards rapid review. Operational facilities will prioritize such projects if they can be accommodated. On behalf of the iNEXT-Discovery team, Hans Wienk (Project Manager) - email h.wienk.AT.nki.nl<http://h.wienk.at.nki.nl/> for questions about access Anastassis Perrakis (Coordinator)

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covalently linked ligand
by Muhammad Bashir Khan 15 Apr '20

15 Apr '20

Hi All; I have a protein molecule and a ligand structure. I want to make a covalent bond between the ligand and protein molecule, could somebody explain to me how I can do that using phenix. I used the " *phenix.ligand_linking pdb_file_name" commond* It creates apply_link.def and data_link.cif I did refine the structure again giving the above file as well but did not see any covalent bond created between the protein and ligand. Thanks for your help Bashir -- ------------------------------------------------------ Muhammad Bashir Khan, Ph.D. Research Associate Department of Biochemistry Medical Science Bldg. Lab 3-27 University of Alberta Edmonton AB, T6G 2H7 Phone: 780-492-4577- e-mail: mbk(a)ualberta.ca <cbrooks1(a)ualberta.ca>

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helix/sheet outliers
by Casper Larsen 14 Apr '20

14 Apr '20

Hi.. I am doing real space refinement on a protein model build from a cryo-em map. I run the refinement with Amber gradients turned on and with secondary structure restraints (otherwise, more or less default settings). I have some issues with helix and sheet outliers. Every time I run the refinement (after making sure that the bond distance in the helices are within the 3.5 Å) I get a lot of bad annotation remarks, but with outliers just above 3.5 Å (see .log below): ... removed outlier: 3.576A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 3.681A pdb=" N PHE A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.737A pdb=" N MET A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) ... Is this something that I just need to fix in several rounds of refinement or is there an explanation? Amber gradients maybe? In addition, I have some bad sheet annotations such as: ... removed outlier: 6.987A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL B 442 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 431 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ALA B 444 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N THR B 429 " --> pdb=" O ALA B 444 " (cutoff:3.500A) ... When I look at the model, the residues are definitely a part of the sheet - the long distance between the N-O atoms is due to the O being "flipped" (hope it makes sense). Is this because of wrong annotation? Best Casper

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