- phenixbb - phenix-online.org

mmCIF output by phenix.refine
by Mark Saper 01 Jul '22

01 Jul '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 22 Jun '22

22 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 15 Jun '22

15 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 09 Jun '22

09 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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Structural Biology position at Odyssey Therapeutics (Boston MA)
by Chip Lesburg 07 Jun '22

07 Jun '22

Opportunity for a Senior/Principal Scientist at Odyssey Therapeutics in Boston MA. We are seeking a highly motivated and skilled Structural Biologist to join the Odyssey team at our site in Boston where you will be a key contributor to the structural enablement of pipeline discovery projects. You will employ cutting-edge structural techniques such as cryo-EM and X-ray crystallography in a cost-effective, efficient manner. You will use your expertise to better understand mechanisms of action and structural aspects of protein-protein and protein-ligand interactions, and to guide protein therapeutic design. You will oversee the production of quality proteins in support of biophysical and structural analyses. Working closely within therapeutic project teams, you will determine and communicate the structures of both protein-small molecule complexes and multiprotein complexes. In this primarily lab-based role, you will be a key contributor to the application of internal and external resources and capabilities necessary to drive biophysics and structural biology efforts. More information, including responsibilities and desired skills, can be found at: https://boards.greenhouse.io/odysseytherapeutics/jobs/4538034004 Chip Lesburg [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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Problem with rebuild_predicted_model
by Andrei Moiseenko 04 Jun '22

04 Jun '22

Dear all, I am trying to build the model with Alphafold2 using Dock and Rebuild and encountered some issue with rebuild_predicted_model. It does not rebuild the model telling that: "Unable to morph model...may not match exactly in chain ID or residue numbers. No morphed model obtained... No docked model to work with." I use the model predicted with Alphafold2 google colab and the cryoem map with 3.5A resolution boxed around the protein of interest. The process_predicted_model and dock_predicted_model run successfully, giving the single-chain model which nicely fits into the map (40 of 300 residues are excluded due to low LDDT). The chain ID in the docked model is indeed different from predicted model: the predicted model has one chain A, but the docked one has A1. However, manually changing the chain ID either in the predicted or in the docked model does not resolve the issue. Manual runs of rebuild_predicted_model also fail with the same result. Tried it with models and maps for different proteins, tried both on Linux and Windows - it gives the same output (Phenix 1.20.1.-4487). Please, find the log attached. I am seeking for any advice on resolving this problem. Best regards Andrey Moiseenko Electron Microscopy Lab @ Biology Department Moscow State University <mailto:[email protected]> postmoiseenko(a)gmail.com skype: callmoiseenko

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