June 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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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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mmCIF output by phenix.refine
by Mark Saper 30 Jun '22

30 Jun '22

Why does .CIF file output by phenix.refine contain all of the -h -k -l reflections. The Bijvoet reflections are already contained in the _refln.pdbx_F_minus column of the +h +k +l reflections. When OneDep at PDB reads in these files, it finds ‘?’ in about half of the reflections, and assigns them a status of ‘x': Warning: (data block=1): 36739 reflections have status assigned as '?' (changed to 'x') Warning: (data block=1): 36739 reflections have wrong status. Not in list(o,f,x,-,<,h,l) Is this the correct behavior? My space group is 19. Thanks, 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

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3x4 matrix for wwPDB deposition
by Christian Tüting 28 Jun '22

28 Jun '22

Hi Phenix Dev team and mailing list recipients, i have a question regarding the 4x3 matrix in the wwPDB deposition assembly tab. I am wondering, if there is an easier way, than what I am currently doing. This is my current workflow: # get the map symmetry phenix.map_symmetry symmetry=O map.mrc # apply symmetry on monomer phenix.apply_ncs mono.pdb symmetry_from_map.ncs_spec # get biomt from complex phenix.find_ncs apply_ncs.pdb # isolate wwPDB deposition 3x4 matrix awk '{print substr($0, 25)}' find_ncs.biomt > 3x4_matrix And this feels a bit redundant, as I already have the symmetry operation directly from the beginning, but the monomeric localization is missing. Is there an easier way to get the 3x4 matrix? This is still fast, so this is fine, but maybe there is an easier, single line solution. Best Christian

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Running phenix into a M1 apple processor
by Armando Albert 24 Jun '22

24 Jun '22

Dear all, Is there any version of phenix for the new M1 apple processors? Thank you Armando

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Building DNA into the cryo-EM map density
by Yangqi Gu 21 Jun '22

21 Jun '22

Dear PHENIX users and developers, I am currently building a model for a cryo-EM map of a helical complex. I could build the protein easily into the map. However, the map also contains a long chain of DNA density, I am wondering what could be the best way to build this DNA model? I have no previous experience building models with a DNA complex, therefore any suggestion would be helpful! Best. Yangqi -- Yangqi Gu Ph.D. Yale University, West Campus

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ACA hotel block closing June 17
by Anna Gardberg 14 Jun '22

14 Jun '22

Dear Colleagues, The ACA annual meeting in Portland is fast approaching. The meeting will be held from July 29 - August 3, 2022. The hotel room block at the Marriott Downtown Waterfront will be closing on June 17th. Book your room today <https://book.passkey.com/event/50263127/owner/3508/home>! Register for the meeting <https://www.acameeting.com/registration-info> and consider taking one of the workshops <https://www.acameeting.com/workshops> on July 29. WK1: Applications of Small Angle Scattering to Structural Biology: An Introduction WK2: Crystallographic and cryo-EM Structure Solution with Phenix WK3: Cryo-Electron Tomography: State of the Art Methods WK4: Hands-on Single-Particle Cryo-EM Data Analysis with Cryo EDU WK5: CryoEM Sample Preparation Training using Center Merit Badges WK6: Advanced Software Tools for Single Crystal Diffraction WK7: Visualizing Structure WK8: Microcrystal Electron Diffraction (MicroED) If you are already registered for the proximally located M&M conference, you can register for the ACA workshops and/or an ACA one day pass <https://acas.memberclicks.net/index.php?option=com_mcform&view=ngforms&id=2…> . We look forward to seeing you in Portland! The 2022 Annual Meeting Committee

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phenix.douse, resampled map?
by Guenter Fritz 12 Jun '22

12 Jun '22

Dear Pavel, dear all, I was running phenix.douse on a map from resolve. It works very nicely. As far as I understand phenix.douse generates a resampled map with finer grid for water picking. Is there an option to write this resampled map out? Best regards, Guenter

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high R-value with resolve_cryo_em
by Daniel Larsson 11 Jun '22

11 Jun '22

Hi all, I tried to do density modification using the resolve_cryo_em tool. The resolution improves quite a lot from around 2.60 to around 2.35 and the density looks significantly better than the autorefined original map. However, the R-values is close to 0.5, which seems very high. How should the R-value generated by this tool be interpreted? It is very poorly documented and not mentioned in the paper or on the manual page, but Tom Terwilliger mentioned in a workshop that “low number is good” and “point two-four is a very good number, point five is not a good number”, which makes me worried. 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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Postdoctoral position in Manchester
by Harshwardhan Poddar 08 Jun '22

08 Jun '22

Hi everyone, There is a PostDoc position available in the laboratory of Prof Nigel Scrutton based at Manchester Institute of Biotechnology. This is an exciting opportunity to characterise some newly discovered light-sensitive proteins using time-resolved structural techniques. More details can be found here- Research Associate in Structural Biology : Manchester Institute of Biotechnology (MIB) | | | | | | | | | | | Research Associate in Structural Biology : Manchester Institute of Biotechnology (MIB) | | | | Best Harshwardhan

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