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CCN submissions and current issue
by Nigel Moriarty 06 Apr '22

06 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 31 Mar '22

31 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 24 Mar '22

24 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 19 Mar '22

19 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 10 Mar '22

10 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 09 Mar '22

09 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 04 Mar '22

04 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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