- phenixbb - phenix-online.org

Validation of structure with modified residue
by Xavier Brazzolotto 21 Apr '22

21 Apr '22

Dear Phenix users, I don’t know if my problem is related to Phenix but for information I’m running Phenix 1.20.1-4487 under MacOS 12.3.1. I’ve finalized a structure where a ligand covalently modified the protein. I’ve generated the modified residue (named SLG for serine modified by ligand). For this I’ve generated the molecules in SMILES and used eLBOW to generate the restraints. Then I’ve modified the cif file defining the molecule as a L-peptide and replacing the atom names of the Serine part (CA, CB, OG, C, O, N, and OXT) In coot (from CCP4 : 0.9.6 EL), I’ve used the modified cif file and it allowed merging of the modified residue into the polypeptide chain as expected and further refinements went without any issue in Phenix (providing the modified cif file of course). Everything seems well interpreted. So far so good. However, now I would like to validate the structure and both Phenix validation tool and the PDB web server do not accept the final cif file. Checking this file I’ve noticed that the protein seems split into 3 pieces (chain A, first residue up to the one before the modified residue; chain B the modified residue by itself described as HETATM and chain C the rest of the polypeptide up to the C-ter). The PDB file presents only one chain A for the whole protein with the modified residue... I don’t know if this is an issue with Phenix generating this final cif file in this specific case or if I need to modify this final file by hand ? Any help is welcome. Thanks Xavier

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ligand at two-fold
by Patrick Loll 14 Apr '22

14 Apr '22

Hello all, I have a dimer in which the two protomers are related by a crystallographic 2-fold. There is a peptide ligand that sits in the interface between the two protomers. This means that the ligand will be present in two orientations, and I’ve set the occupancies to 0.5. However, the ligand is pushed out of density during refinement, presumably because orientation #1 is repelling orientation #2 (to be clear, orientations #1 and #2 are symmetry mates). To deal with this, I include a parameter file in the GUI that contains the following instruction: custom_nonbonded_symmetry_exclusions = "chain X” [where chain X is the peptide ligand] However, the refinement fails, with the following error message: "Unused parameter definitions: Please check the input file(s) for spelling errors and obsolete parameter definitions." This would seem to imply that the custom_nonbonded_symmetry_exclusions command is obsolete, but it’s still found in the list of all available keywords (?). Any help would be welcome. Thanks, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. (he, him, his) Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102 USA pjl28(a)drexel.edu pjloll(a)gmail.com

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Error from exceeding max reasonable bond distance
by Mullins, Elwood A. 13 Apr '22

13 Apr '22

I’m having an issue with a real-space refinement job crashing after giving the following error: "RuntimeError : Bond distance > max_reasonable_bond_distance: 62.8014 > 50". I found mention of this problem in a post from 2017. I tried the recommended solution (setting the max reasonable bond distance to 999), but that caused the job to hang. I also tried clicking “proceed with excessive length bonds”. That didn’t make a difference; I received the same error message. I ran validation on the model. There are no bond length outliers and only minor other issues. Any help would be greatly appreciated. Thanks, Elwood

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The lowest resolution score X-ray statics resolution bin is lower than overall datasets.
by Takebe Katsuki 11 Apr '22

11 Apr '22

Dear all, I am working on a 20 KD protein and We scaled the data sets 1.6Å. The lowest resolution score X-ray statics resolution bin is lower than overall datasets. Is this seriously problem? and How do I solve the problem? Could you give me some advice on this problem? DATA USED IN REFINEMENT. RESOLUTION RANGE HIGH (ANGSTROMS) : 1.600 RESOLUTION RANGE LOW (ANGSTROMS) : 44.488 　 [cid:[email protected]]

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2022 ACA session on AI predicted Models in Structural Biology/Crystallography
by Aaron Brewster 11 Apr '22

11 Apr '22

Hi all, we'd like to call your attention to the upcoming session at the 2022 ACA on the use of AI predicted Models in Structural Biology/Crystallography. We'd like to invite abstract submissions to this session from people, including early-career scientists, who have done difficult or interesting work using these AI predicted structural models, such as from AlphaFold2 and RoseTTAFold. We are very excited to hear what people are using these tools for and how the future might unfold in this new world of AI-aided structural analysis and design. Remember that the deadline to submit an abstract for talks is April 15, 2022@ 11:59 PM ET. The full abstract for the session is below. Thanks, -Aaron Brewster and John Moult Prediction of 3D protein structure by AlphaFold2 and RoseTTAFold has achieved revolutionary accuracy using new AI methods. These programs can accurately predict the 3D structure of many proteins from 1D amino acid sequences, opening up a vast array of exciting new experiments and challenges for researchers. In this session we will explore current applications of these structures in molecular replacement, cryo-EM fitting and refinement, structure-based drug design, and tomography. We will explore what kinds of new and difficult methods have been enabled and what remains difficult. Other topics may include how error estimates on AI protein models can be incorporated into these methods, progress in modeling of protein complexes, implications of AI structures on protein design, the generation and use of structure ensembles, and new data analysis best practices that need to be developed as the use of computer-generated structures becomes more common. Sponsored by the BioMAC and Best Practices for Data Analysis and Archiving SIGs

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The lowest resolution score X-ray statics resolution bin is lower than overall datasets.
by Takebe Katsuki 11 Apr '22

11 Apr '22

Dear all, I am working on a 20 KD protein and We scaled the data sets 1.6Å. The lowest resolution score X-ray statics resolution bin is lower than overall datasets. Is this seriously problem? and How do I solve the problem? Could you give me some advice on this problem? DATA USED IN REFINEMENT. RESOLUTION RANGE HIGH (ANGSTROMS) : 1.600 RESOLUTION RANGE LOW (ANGSTROMS) : 44.488 　 [cid:[email protected]]

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Fragment-based drug discovery session at ACA 2022
by Tanner, John J. 08 Apr '22

08 Apr '22

As many of you know, the 2022 ACA meeting will be held in Portland, OR on July 29 to August 2. I would like to draw your attention to the session on fragment-based drug discovery and invite you to submit an abstract for an oral presentation. We welcome contributions from students as well as PIs. The Abstract deadline is April 15. https://www.acameeting.com/ Session details: 3.2.2 Fragment Based Drug Discovery 8/1/2022 @ 2:00:00 PM - 5:00:00 PM Sponsoring SIG(s): Industrial Co-Sponsoring SIG(s): BioMac Session Chair(s): Matt Clifton, Jack Tanner Fragment Based Drug Discovery (FBDD) utilizes small molecule compounds to help identify starting points in the drug discovery process. This process allowed for the discovery of lead compounds for difficult protein targets with small/shallow pockets or protein-protein interactions. In contrast to other screening techniques such as High-Throughput Screening (HTS) or DNA-encoded Libraries (DEL), FBDD utilizes small libraries of molecules (< 2000) with molecular weights less than ~200 Da. FBDD has been key in the development of multiple approved drugs and dozens of other drugs in clinical trials. This session will focus on the biophysical and structural techniques used in FBDD to identify initial starting points, optimization by fragment growing/linking, and the route to lead optimization. -- John J. Tanner Professor of Biochemistry and Chemistry Associate Chair of Biochemistry Department of Biochemistry University of Missouri 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Email: tannerjj(a)missouri.edu<mailto:[email protected]> https://cafnrfaculty.missouri.edu/tannerlab/ Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A

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CCN submissions and current issue
by Nigel Moriarty 05 Apr '22

05 Apr '22

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 1 JUN 2022. Please consider writing an article of general interest to the community. 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 is attached to this email. Current Issue: January 2022 Full issue <https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CC…> Articles: - Extreme backbone outlier patterns when AlphaFold gives up <https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CC…> - Difference Density Tracer: A Tool for Rapid Visualization of Difference Densities in Proteins to identify Dynamics <https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CC…> Fitting Tips: - Fitting tips #22 – Places where you should never fit a cis-nonPro peptide <https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CC…> 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 ORCID : orcid.org/0000-0001-8857-9464

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Question about RMSD vs e/A^3
by Vatsal Purohit 30 Mar '22

30 Mar '22

Hi all, I had a question about comparing structures based on RMSD comparisons vs e-/A^3. While the former seems to be more frequently used in structural studies with a standard value of 1.0 rmsd for 2Fo-Fc and 3.0 rmsd for Fo-Fc, there are differences in RMSD based on resolution. Hence, I wanted to ask if e-/A^3 could be a more appropriate comparison for looking at differences in electron density in a ligand-binding site between 2 structures of the same enzyme? So, here you would try and set e-/A^3 of all the maps (2Fo-Fc and Fo-Fc) to the same value. The structures I’m referring to are between 2-2.5 angstroms in resolution. I have also worked with the map sigma level comparison tool on PHENIX and wanted to know if that might be an alternate way to compare maps in 2 structures accordingly. Regards, Vatsal Post-doctoral fellow, Davis Lab, Emory University vatsal.purohit(a)emory.edu <mailto:[email protected]> | 346-719-9409

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Phenix.refine question
by Mark Saper 23 Mar '22

23 Mar '22

Laurie, Really bizarre. The experts will have more info, I hope. When you model the Tyr in the posiive density, is the geometry satisfactory (including main-chain)? If so, then you might try turning off real space refinement and see what happens. Check the occupancies of the Tyr also. -Mark _____________________ Mark A. Saper, Ph.D. Associate Professor Emeritus of Biological Chemistry University of Michigan Medical School saper(a)umich.edu | +1 734 276 6505 Powered by Mailbutler <https://www.mailbutler.io/?utm_source=watermark&utm_medium=email&utm_campai…>, the email extension that does it all

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Phenix.refine question
by lbetts0508 18 Mar '22

18 Mar '22

I am refining a small protein crystal model with 1.3 A data, there is a Tyrosine that won't stay put where it looks to me it should go (see below in it's original position, in the negative density; I moved the ring into the positive Fo-Fc density). After I move it into the positive density, save the coordinates, and do another refinement with the new coordinates, I find it right back in the negative density, even if I only refine ADP or OCC. Is there some trivial reason this is happening, or can I tell it to not refine that residue? https://docs.google.com/document/d/1RkZSH312q2Pimxb9gKLjibm1XbpsVpyzmrX4wGx… THanks Laurie Betts

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Postdoctoral position in the MRC Laboratory of Molecular Biology
by Roger Williams - MRC LMB 16 Mar '22

16 Mar '22

Our group has an opening for a postdoctoral fellow to be funded on a Cancer Research UK programme aimed at understanding lysosomal control of cell proliferation and stress responses in cancer cells. The programme involves cryo-electron microscopy, X-ray crystallography, H/D exchange mass spectrometry, molecular dynamics as well as other biophysical and biochemical approaches. The post will focus on the reconstitution of large signalling assemblies that detect nutritional and stress signals on and off membranes. The candidate will join a vibrant team of researchers investigating structures, regulation, kinetics and dynamics of phosphoinositide 3-kinase family members reconstituted with their regulators on membrane surfaces. This programme concerns regulation of the lipid kinase VPS34 and protein kinase mTOR and ATM-containing complexes. The research combines biochemical, biophysical and cell biological methods with structural approaches. This is a unique opportunity to play a major role in exciting programme, introduce new ideas, and disseminate research results, while working in a collaborative and supportive environment. The position is available immediately, with an application closing date of 11 April 2022. For more details, please see https://www.nature.com/naturecareers/job/postdoctoral-scientist-pnac-dr-rog… <https://www.nature.com/naturecareers/job/postdoctoral-scientist-pnac-dr-rog…> Please contact Roger Williams at rlw(a)mrc-lmb.cam.ac.uk <mailto:[email protected]>, if you have any questions. Dr. Roger Williams, FMedSci, FRS rlw(a)mrc-lmb.cam.ac.uk MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Phone: +44 1223 267094

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Molecular replacement of cyclic polypeptide with non-standard amino acid
by Ariela Samantha 09 Mar '22

09 Mar '22

Dear all, I have collected an XRD data from a crystal of cyclic polypeptide with non-standard amino acid (2,4-diaminobutyric acid). Is it possible to solve the structure by molecular replacement? Or does anyone have any suggestion for solving the structure? Thank you very much for your kind help. --- Best regards, Ariela Samantha PhD Candidate Department of Structural Biology School of Molecular Sciences The University of Western Australia Bayliss Building room 4.26 Phone +61 8 6488 ext. 3163

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Error message on minimization global
by Abhipsa Shatarupa 08 Mar '22

08 Mar '22

Hello, I am a beginner in phenix. Currently, I am running minimization global under real-space refinement. The input files for this job are a .pdb file generated from rigid-body refinement and a .ccp4 map. I end up receiving the following error message (image attached -Error file). The output log file gives me the description of the number of atoms and the atoms responsible for generating the error (image attached – atoms file). I ended up finding a couple of Q/A on a similar error message, but I am not sure how to generate the CIF file to overcome the problem using eLBOW? Could someone please help me resolve this issue? Thanks in advance, Abhipsa

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XChem access: Diamond AP32 Call for Proposals open until 30 March 2022
by Fearon, Daren (DLSLtd,RAL,LSCI) 08 Mar '22

08 Mar '22

Hi all, Friendly reminder that the Diamond AP32 call for proposals (which includes XChem access between October 2022 and March 2023) is open until Wednesday 30th March at 17:00hrs UTC/GMT+1. Please check our webpage<https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening/XChem-Applicati…> for more details and if you have any questions about applying then do get in touch. Cheers, Daren Dr Daren Fearon (he/him) Senior Beamline Scientist (XChem) Diamond Light Source Ltd Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE Tel: 01235 778936 Mobile: 07425638147 Email: daren.fearon(a)diamond.ac.uk<mailto:[email protected]> Web: www.diamond.ac.uk/Instruments/Mx/Fragment-Screening.html<http://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening.html> [https://gallery.mailchimp.com/3de94671e0e91f373e1995d94/images/557065e4-53a…] Reminder: Diamond – AP32 Call for Proposals Dear Colleague, This is a gentle reminder that our call for proposals for AP32 is open and the deadline for this call is Wednesday 30th March at 17:00hrs UTC/GMT+1. The period will cover October 2022 to March 2023. Please note that as this is in working hours the call will be closed at this time. A table of instrument access is given here<https://www.diamond.ac.uk/Users/Apply-for-Beamtime.html>. Users from the EU: Submitting proposals and visiting Diamond post-Brexit Users from European organisations continue to be welcome to submit proposals to Diamond. The same funding policy and procedure for expenses continue to be in place for any visit to Diamond as was in place before Brexit. You can find our expenses procedure here.<https://www.diamond.ac.uk/Home/Legal-and-Compliance/Procedures/Financial-Su…> Proposal Information The science case and reporting templates have been updated. You are strongly encouraged to use the most up-to-date template available for download in the User Administration System. Experiments that can be completed remotely or by mail-in should be highlighted. Please refer to the relevant information that each of the beamlines have published. You will find relevant information under each instrument’s specific information here.<https://www.diamond.ac.uk/Instruments.html> Do discuss your planned work with our instrument scientists and submit all proposals to UAS<https://uas.diamond.ac.uk/>. In addition, please ensure that any outstanding reports are submitted, and that your publications related to your previous beamtimes are in our database<http://publications.diamond.ac.uk/> as the peer review panel will take these into consideration during the review. A number of additional instruments will be taking submissions for proposals: I06<https://www.diamond.ac.uk/Instruments/Magnetic-Materials/I06.html> - Laser-PEEM/LEEM Facility for Multidisciplinary Nanoscience Imaging: A new multidisciplinary nanoscience imaging facility, using PhotoEmission Electron Microscopy (PEEM) and Low-Energy Electron Microscopy (LEEM), will be available for peer-reviewed access starting in AP32 (from October 2022). PEEM gives nanoscale insights into the magnetic properties of materials whilst LEEM provides detailed nanoscale structural insights through full-field imaging combined with spatially resolved Low-Energy Electron Diffraction (micro-LEED). The facility combines PEEM/LEEM with a continuous wave (CW) laser (Laser-PEEM/LEEM) providing high spatial resolution with probing depths ranging from less than a nanometre to tens of nanometres. To submit a proposal please select I06 in submission process. Further details are available from Dr. Sarnjeet Dhesi (dhesi(a)diamond.ac.uk<mailto:[email protected]>). The multidisciplinary Laser-PEEM/LEEM facility is funded by Diamond Light Source and the Engineering and Physical Sciences Research Council (EPSRC Grant: EP/V029258/1) and is being developed in collaboration with the Central Laser Facility, the University of Oxford, the University of Cambridge, the University of Nottingham and University College London. ________________________________ Diamond's new Active Materials Laboratory<https://www.diamond.ac.uk/Science/Integrated-facilities/active-materials-la…> (AMLab) is in the process of being fitted out and is now ready for use. Users who want to use this facility in their proposals will be able to select it as an instrument in UAS<https://uas.diamond.ac.uk/>. ________________________________ DL-SAXS<https://www.diamond.ac.uk/Instruments/Soft-Condensed-Matter/small-angle/Off…> - The Offline SAXS instrument, Xeuss 3.0<https://www.xenocs.com/saxs-products/saxs-equipment-xeuss/>, from Xenocs<https://www.xenocs.com/>, has been delivered with both Excillium Gallium MetalJet and Molybdenum Microsource options. The instrument has a set of sample holders<https://www.diamond.ac.uk/Instruments/Soft-Condensed-Matter/small-angle/Off…> available for use. Please discuss any ideas for Sample Environment driven experiments with a member of the team<https://www.diamond.ac.uk/Instruments/Soft-Condensed-Matter/small-angle/Off…> before submitting. ________________________________ B07<https://www.diamond.ac.uk/Instruments/Structures-and-Surfaces/B07.html> – When submitting proposals for B07 the award will be assigned by the beamline staff<https://www.diamond.ac.uk/Instruments/Structures-and-Surfaces/B07/Staff.html> to the branch line (B07-B or B07-C) which is optimal for a given experiment. Please select B07 when you submit your proposal with a view to beamline staff determining which of the two branch lines, B07-B and B07-C, will be the optimal choice. Applicants are encouraged to discuss the options with the beamline staff before submission and will be able to express their preference in the “beamline questionnaire” part of the proposal form. ________________________________ DIAD<https://www.diamond.ac.uk/Instruments/Imaging-and-Microscopy/DIAD.html> - The Dual Imaging and Diffraction (DIAD) beamline is a dual beam X-ray instrument for imaging, diffraction and scatterin g, which operates at energies of 7-38 keV. Information and questions to consider when writing the proposal can be found on the DIAD web-pages. ________________________________ I08<https://www.diamond.ac.uk/Instruments/Imaging-and-Microscopy/I08.html> has extended its portfolio with a new instrument for soft X-ray ptychography (I08-1). When submitting proposals for I08 the award will be given for that instrument with a view to beamline staff determining which of the two instruments will be the optimal choice for a given experiment. Please contact Burkhard Kaulich<mailto:[email protected]> (I08 PBS) for further information. Best wishes, Diamond User Office [Diamond Light Source Logo]<https://www.diamond.ac.uk/> Diamond Light Source is the UK's national synchrotron science facility, located at the Harwell Science and Innovation Campus in Oxfordshire. [Follow Us on Twitter]<http://www.twitter.com/DiamondLightSou> [Website]<https://www.diamond.ac.uk/> Copyright © 2022 Diamond Light Source, All rights reserved. Our mailing address is: Diamond Light Source Diamond House Harwell Science & Innovation Campus Didcot, Oxfordshire OX11 0DE United Kingdom Add us to your address book<https://diamond.us20.list-manage.com/vcard?u=3de94671e0e91f373e1995d94&id=7…> You are receiving this email because you are registered in our User Administration System (https://uas.diamond.ac.uk). If you would like to opt out of future bulk emails, please click unsubscribe<https://diamond.us20.list-manage.com/unsubscribe?u=3de94671e0e91f373e1995d9…>. Please note that unsubscribing from this mailing list will not stop you from receiving operational emails related to your upcoming visits or essential information related to your account. If you wish to update your personal information, please do so directly in the User Administration System (https://uas.diamond.ac.uk<https://uas.diamond.ac.uk/>). For more information about our privacy policy, please visit www.diamond.ac.uk/Legal<http://www.diamond.ac.uk/Legal.html>. -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Online Workshop Series on Structural and Crystallographic Databases -- Registration Open
by Mitchell D. Miller 03 Mar '22

03 Mar '22

On behalf of The U.S. National Committee for Crystallography (USNC/Cr) of the National Academies of Sciences, Engineering, and Medicine, I am happy to announce that registration is now open for "EXPLORING STRUCTURAL DATABASE USE IN CRYSTALLOGRAPHY: WORKSHOP SERIES". The topics will focus on using, developing, and maintaining crystallographic and structural databases- encompassing macromolecular, small molecule, and powder diffraction. We will open the series with a keynote delivered by John Helliwell (IUCr Chair of the Committee on Data) on March 21, 2022 followed by 10 one-day and two-day workshops focused on 8 different structural and crystallographic data resources. An overview of the program can be found in the attached PDF. Graduate students, postdoctoral fellows, faculty members and researchers in any of the crystallographic, diffraction, and imaging sciences affiliated with the International Union of Crystallography (IUCr) are encouraged to register and participate in the training sessions that interest them. Registration for this online series is free. To read more about each session and to register, please visit: https://www.nationalacademies.org/our-work/exploring-structural-database-us… The details about each session can be found by clicking the event pages along with a registration link allows one to register for any combination of the 1 and 2 day sessions (each meeting for 2-4 hrs/day). The workshop series is sponsored by the National Institute of Standards and Technology (NIST). For more information, please contact Ana Ferreras, Telephone: (202) 334-1697 Email: aferreras(a)nas.edu[1] Sincerely, Mitch Links: ------ [1]

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Coot opening problem
by Afshan Begum 03 Mar '22

03 Mar '22

Hi Expert, I am refinening my strcuture on phenix , Could you kindly suggest me why after refinement in phenix (version i used 1.9-1692, Mac operation system) COOT does not open up by clicking on COOT button.Its seems open but only black screen (or blank window) come up without out any data, As previously always its open very smoothly , so now i have to open all files manually every time. Best Regards =============================== Afshan Begum

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Output MTZ file from Phenix Refine
by Mark Saper 02 Mar '22

02 Mar '22

Thanks to Tom the issue is resolved. If I examine the MTZ file with phenix.mtz.dump the angles are in degrees as they should be. For some reason CCP4 ViewHKL program shows them in radians although they are stored internally as degrees. > The output MTZ from Phenix refinement contains F-model and PHIF-model. I wanted to use the PHIF-model term in CCP4 but I discovered that PHIF-model in a Phenix mtz is in radians while CCP4 expects degrees. Why the discrepancy? > > -Mark _____________________ Mark A. Saper, Ph.D. Associate Professor Emeritus of Biological Chemistry University of Michigan Medical School saper(a)umich.edu | +1 734 276 6505 Powered by Mailbutler <https://www.mailbutler.io/?utm_source=watermark&utm_medium=email&utm_campai…>, the email extension that does it all

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Output MTZ file from Phenix Refine
by Mark Saper 02 Mar '22

02 Mar '22

The output MTZ from Phenix refinement contains F-model and PHIF-model. I wanted to use the PHIF-model term in CCP4 but I discovered that PHIF-model in a Phenix mtz is in radians while CCP4 expects degrees. Why the discrepancy? -Mark _____________________ Mark A. Saper, Ph.D. Associate Professor Emeritus of Biological Chemistry University of Michigan Medical School saper(a)umich.edu | +1 734 276 6505 Powered by Mailbutler <https://www.mailbutler.io/?utm_source=watermark&utm_medium=email&utm_campai…>, the email extension that does it all

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Call for Topical review articles for Acta Cryst F Structural Biology Communications
by John R Helliwell 25 Feb '22

25 Feb '22

Dear Colleagues, We draw your attention to our call for Topical review articles for Acta Cryst F Structural Biology Communications described here:- https://journals.iucr.org/f/issues/2021/11/00/me6156/index.html We welcome your proposals. Best wishes, John, Mark and Janet John Helliwell, Mark van Raaj and Janet Newman Emeritus Professor John R Helliwell DSc

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General interest
by John R Helliwell 02 Feb '22

02 Feb '22

Dear Colleagues, I imagine you would be interested in the book “Collecting Experiments. Making Big Data Biology” which I have reviewed here:- https://journals.iucr.org/j/issues/2022/01/00/xo0187/index.html My book review is open access. I have dedicated my book review to John Westbrook. Best wishes, John Emeritus Professor John R Helliwell DSc

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PhD fellowship at NC State & Oak Ridge National Laboratory
by Meilleur, Flora 25 Jan '22

25 Jan '22

Thank you for sharing the following PhD opportunity with interested students! Best wishes, Flora PhD fellowship in Structural Biology of Metalloenzymes at NC State & Oak Ridge national Laboratory A Ph. D. research fellowship (up to 5 years) in enzyme chemistry is available with Dr. Flora Meilleur. The position is joint between North Carolina State University, the Ph. D. granting institution where the Ph. D. candidate will complete the program core coursework, and Oak Ridge National Laboratory, where research activities will be performed. The project will focus on lytic polysaccharide monooxygenase, a class of copper containing metalloenzymes involved in biomass oxidation. High resolution X-ray and neutron crystallography will be used primarily to study the enzymatic mechanism. The project will involve collaborations to include spectroscopic and biophysical methods as well as computational approaches. Key publications on the topic include (complete list here<https://scholar.google.com/citations?user=i0aLPhYAAAAJ&hl=en>): Schröder G.C., O'Dell W.B., Webb S.P., Agarwal P.K., and Meilleur F. (2021) Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase. ChemRxiv. 10.26434/chemrxiv-2021-n4c1x<https://chemrxiv.org/engage/chemrxiv/article-details/61b3cdd8689c875d6adea9…> O'Dell W. B., Aggarwal P., Meilleur F. (2017) Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase. Angew. Chem. Int. Ed. 56:767-770<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340418/> The candidate should hold a degree in chemistry or biochemistry. Prior experience in molecular biology, protein expression, or protein purification is an advantage. The position is available now and applications are welcome until the position is filled. Interested candidates must email a detailed CV, a letter of motivation and the name of three scientists for reference to Flora Meilleur<mailto:[email protected]?subject=Application%20to%20NC%20State%20/%20ORNL%20PhD%20Fellowship> prior to applying to the Graduate Program in Biochemistry at NC State. For further information about the position, interested candidates can contact Flora Meilleur<mailto:[email protected]?subject=Questions%20about%20NC%20State/ORNL%20PhD%20Fellowship>. Further information about the NC State Biochemistry graduate program here<https://cals.ncsu.edu/molecular-and-structural-biochemistry/>. Further information about the neutron facilities at Oak Ridge National Laboratory here<https://neutrons.ornl.gov/>.

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refining a covalent-bound ligand (part 2)
by Sergio A. Sampieri 22 Jan '22

22 Jan '22

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refining a covalent-bound ligand (part 2) (try 2)
by Sergio A. Sampieri 22 Jan '22

22 Jan '22

Hi all, hope this message finds you well. As in a previous topic from 2018, I’m having problems refining a covalent-bounded ligand. The link shall be made between a carbon atom that is double bonded to an oxigen “SMILES C1=CC=C(C=C1)C=O” and the SG group of a Cys residue. I generated a CIF dictionary through AceDRG in COOT and CCP4i2. But after trying different approaches during refinement, (Automatic Linking parameters, Atom selection, acceptor & donnor, ligand bond cut off and so) the result keeps being a non bounded enzyme-ligand complex (“Not linked: pdbres="LIG A 401”). I readed in the phenixbb that this was solved by changing the nature of the ligand ( http://www.phenix-online.org/pipermail/phenixbb/2018-February/023718.html), but is not the way I would like to follow. Any suggestions or ideas would be greatly appreciated, thanks a lot for your time. Stay safe. -- “I’ve learned to think like a virus; no neurons, a lot of sex, and a lot of errors.” John J. Holland Biól. Sergio Aguirre Sampieri

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AlphaFold changes everything": new lecture on the Phenix tutorials channel
by Dorothee Liebschner 22 Jan '22

22 Jan '22

Hi everyone, I hope you will like "AlphaFold changes everything <https://www.youtube.com/watch?v=9IExeA_A8Xs>", the latest addition to the Phenix tutorials channel at www.youtube.com/c/phenixtutorials. In this full-length lecture, Tom Terwilliger shows how AphaFold models are great hypotheses that can help you jump-start structure determination by X-ray crystallography and Cryo-EM. The talk is from the ReNaFoBis.FRISBI webinar series organized by Jean Cavarelli (https://www.renafobis.fr/seminaires-web-renafobis). Best wishes, The Phenix team -- 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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