September 2022 - phenixbb - phenix-online.org

RapiData at SSRL 2022 - application deadline extended by two weeks!
by Smith, Clyde 12 Jan '23

12 Jan '23

We have extended the deadline for applications for a place at the RapiData 2022 @ SSRL workshop to next Friday, February 4th 2022! There are still a few spots left, so get your application in! The workshop will be held virtually from May 4 - 14 2022. The course will comprise lectures on the following topics: Specimen preparation, data collection strategies, X-ray light sources, X-ray detectors, data reduction, structure solution by MAD, SAD and molecular replacement, complementary methods (spectroscopy, small angle scattering and cryoEM). There will also be several days of software tutorials (HKL3000,XDS, CCP4/DIALS, Phenix, AutoSharp/AutoProc, Shelx, Coot) and you will all get to connect remotely to the SSRL beamlines to collect both monochromatic and MAD/SAD data. There is also an opportunity to ship your own samples to SSRL prior to the workshop, and collect your own data. Please visit https://www-ssrl.slac.stanford.edu/rapidata/rapidata-2022/index.html and use the links on the "registration" page to apply for the course. Successful applicants will be notified later in February 2022 and invited to register at that time (there will be no fee for registration). Regards, Clyde Smith (csmith(a)slac.stanford.edu) and Silvia Russi (srussi(a)slac.stanford.edu) Workshop Organizers

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2022 MicroED Workshop
by Brent Nannenga 07 Oct '22

07 Oct '22

Dear all, We are pleased to announce the 7th MicroED workshop to be held the evening of December 11th to the 14th, 2022, and will be open to both academia and industry. This workshop will be held at the MicroED Imaging Center at UCLA and will contain both lectures and hands on demonstrations and training. For more information, tentative schedule, and to apply please see the following website: https://cryoem.ucla.edu/course-2022 Space is limited and historically, the workshop is typically oversubscribed, therefore we encourage applications to be sent in early. Topics covered will include all aspects of microcrystal electron diffraction (MicroED) of diverse samples such as soluble proteins, membrane proteins, small molecules, natural products, and other materials. We will cover * Sample preparation methodologies for proteins and small molecules * MicroED data collection * Camera performance * Cryo-FIB-milling procedures for MicroED * Data analysis software, structure solution, and refinement The schedule is available on the registration page. // Sincerely; on behalf of the organizing committee (Tamir Gonen, Brent Nannenga)

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SSRL/LCLS User Meeting Registration is Open
by Mooers, Blaine H.M. (HSC) 29 Sep '22

29 Sep '22

Dear phenixbb: The SSRL/LCLS User's Meeting will be September 26-30, 2022. It will be virtual again due to COVID, but the of the sessions will be recorded live. Registration<https://urldefense.com/v3/__https://events.bizzabo.com/SLAC-UsersMeeting-20…> is free and open to all. We had about 1600 registrants last year. We will have 27 workshops, 3 poster sessions, and 3 plenary sessions. Distinguished plenary speakers include Drs. John Helliwell and Linda Young. Although the registered attendees will be able to view the videos at a later time, please do attend during the live sessions to participate in the question and answer periods. There will be several poster prizes. The BioXFEL prizes are not limited to work done at LCLS. The deadline<https://urldefense.com/v3/__https://events.bizzabo.com/SLAC-UsersMeeting-20…> for the submission of poster abstracts is September 9th. Best regards, Blaine Mooers on behalf of the SSRL/LCLS User's Meeting Organizing Committee and the SSRL User Executive Committee<https://urldefense.com/v3/__https://www-ssrl.slac.stanford.edu/content/abou…> and the LCLS User Executive Committee<https://urldefense.com/v3/__https://lcls.slac.stanford.edu/lcls-users-organ…>

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Alternative to AlphaFold2?
by Chip Lesburg 22 Sep '22

22 Sep '22

Hi PHENIX users, At this past summer's Diffraction Methods GRC meeting<https://www.grc.org/diffraction-methods-in-structural-biology-conference/20…>, Tom Terwilliger presented the utility of incorporating AlphaFold2 predictions during structure fitting and rebuilding. I wonder if anyone has experience using that or an alternative such as OmegaFold<https://www.biorxiv.org/content/10.1101/2022.07.21.500999v1> or OpenFold<https://github.com/aqlaboratory/openfold>? Are any of these easier or harder to get set up? Chip [cid:153156_edd5022b-de61-48a6-bf68-1a41de35ba89.png] Charles Lesburg Vice President, Structural Biology M 908-265-2064 301 Binney Street, Cambridge, MA 02142 odysseytx.com This message is for the named person's use only. It may contain confidential, proprietary or legally privileged information. If you receive this message in error, please immediately delete it and all copies of it from your system, destroy any hard copies of it and notify the sender. ODYSSEY THERAPEUTICS, INC. ("ODYSSEY THERAPEUTICS") reserves the right to monitor all e-mail communications through its networks. ODYSSEY THERAPEUTICS cannot be committed by this e-mail or warrant the accuracy or validity of any information presented. Any views expressed in this message are those of the individual sender.

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Question about occupancy and 2Fo-Fc and Fo-Fc maps
by Vatsal Purohit 20 Sep '22

20 Sep '22

Hi everyone, I had 2 questions regarding occupancy and maps generated in ligand-bound regions for various ligand models potentially present in the structure: 1. I’ve been working with some 2.0 angstrom structures and trying out refinements with 2 sets of bound ligands at varying occupancies (at the same active site) to get an approximate idea of their relative populations in the structure. For one set of ligands, I observe 2Fo-Fc density in regions uniquely occupied by them even when their occupancy is zero. Could there be a reason why this is the case? 2. Additionally, I observe red Fo-Fc density in the same region when the occupancy is set to 1.0. It disappears at lower occupancies of 0.7 indicating that a lower population of this ligand is present. However, when the occupancy is very low, we don’t see an equivalent green Fo-Fc density popping up in the same region. Could there be a reason for why the red Fo-Fc density at high occupancy doesn’t translate to green Fo-Fc for the same region at low occupancy? Any information or resources that could give me more insight into this question would be really helpful! Regards, Vatsal

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General interest article
by John R Helliwell 09 Sep '22

09 Sep '22

Dear Colleagues, I imagine you will find the article “The 4Rs and crystal structure analysis: reliability, reproducibility, replicability and reusability” of interest. The weblink is https://journals.iucr.org/j/issues/2022/05/00/dv5002/index.html The article is open access. It is a Teaching and Education article in J Appl Cryst. Best wishes, John Emeritus Professor John R Helliwell DSc

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Runtime error : Bond distance
by Luca Pellegrini 06 Sep '22

06 Sep '22

Phenix real space refine (dev 4704) crashes with: RuntimeError : Bond distance > max_reasonable_bond_distance: 67.4676 > 50: I’ve found various reports of this error in the bb but no (to me) clear solution, only one suggestion to increase the max_reasonable_bond_distance (Nov 2017). I tried setting excessive_bond_distance_limit (I guess is the same) to 999 but with no success as Phenix stops with the same error. Any help on how to fix this gratefully received. Best wishes, Luca

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Reference model restraints
by Luca Pellegrini 01 Sep '22

01 Sep '22

Hello, Phenix.real_space_refine keeps pushing a residue out of density so I'd like to restrain it to its current position. Can you please let me know how to implement in the GUI the first example at point 14 at https://phenix-online.org/documentation/reference/real_space_refine.html#us… phenix.real_space_refine model.pdb map.mtz \ reference_coordinate_restraints.enabled=true \ reference_coordinate_restraints.selection="chain A and resseq 12:21" \ reference_coordinate_restraints.sigma=0.05 Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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Phenix website downtime
by Billy Poon 01 Sep '22

01 Sep '22

Hi everyone, There was some networking issue which caused the Phenix website to be down for several hours. The site should be back to normal, but please let us know if you have 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 Fax: (510) 486-5909 Web: https://phenix-online.org

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