August 2023 - phenixbb - phenix-online.org

map deposition strategy after density modification
by Daniel Larsson 20 Sep '23

20 Sep '23

Hi Phenix community, I’ve been using density modification with some success for my data and am considering the most appropriate way to do model building/refinement and then deposition of my results. Here are some questions/observations: 1) Which map should I refine against (most importantly, do the final minimization using phenix.real_space_refine)? The DM map is the most clear one, so I’m favoring to do it against this one (as long as the geometry/validation is also best for this one). 2) Which map should I deposit as my main map? Is it the autosharpened one or the DM one? Since the DM map looks the best, I want the user who only downloads one map to see this one, so again I favoring this map. 3) Which nominal resolution should I quote for my reconstruction? Since the procedure seems to introduce correlation between the two maps (see point 4 below), it does not seem to be possible to obtain a gold-standard FSC value between two truly independent half-maps. As the DM procedure supposedly actually improves the map (by leveraging knowledge about what solvent and macromolecular maps usually looks like and thereby improves the Fourier coefficients), it feels like it would be misrepresenting the data by quoting the FSC_0.143 from the original reconstruction. Should I use the FSC_0.5 estimated value that phenix.resolve_cryo_em outputs? 4) Which FSC curve should I deposit? When I calculate the FSC between the two density modified half-maps, I get a funny (or rather not so funny) looking curve with a bump at around 3Å and it does not go to zero at Nyquist (which does not agree with the map quality). This must again be due to the induced correlation between the maps, presumably during the masking of solvent and macromolecule density. Phenix.resolve_cryo_em calculates a FSC curve to calculate the FSC_0.5 value, which according to the manual page corrects for the correlation induced between the two maps: "Density modification introduces some correlations between half-maps due to solvent flattening. This can have a small effect on the resolution estimates obtained with half-map FSC. The resolution estimates provided by the program are corrected for this effect." But is this curve good enough? I think OneDeposit wants to have the gold-standard FSC curve, right? 5) Which (nowadays mandatory) half-maps should one deposit? Here I would say that the original half-maps before DM makes more sense, since these are less processed. But if one specify these as the half-maps, there will be inconsistencies during validation, since the DM map will look quite different from the average between the two original half-maps. Also the automatic FSC curve will be very different from the deposited one. So in conclusion, despite what I say above, the most conservative thing would be to deposit the conventionally sharpened map as my main map and use the original half-maps for calculating the FSC-curve and use the 0.143 threshold from this curve to estimate the resolution. The DM map can be used during rebuilding/refinement, but I think final minimization should be against the main map during deposition (with restraints if the geometry gets worse). The DM map can be deposited as an auxiliary map. Do the community and the developers agree? 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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Phenix presentation at IUCr Melbourne Software Fayre
by Dorothee Liebschner 25 Aug '23

25 Aug '23

Hi everyone, For those of you attending the IUCr conference in Melbourne, please note the following presentations at the Software Fayre. Talks in the Software Fayre are unfortunately not listed in the conference app, so I advertise it here. "Phenix - Macromolecular structure determination using crystallographic and cryo-EM data" (*Dorothee Liebschner*) When: Saturday, 8/26, 12:45 - 13:30pm Where: Room 214 Topics include: - Introduction to Phenix - What's new - Using predicted models for Crystallography "Physics-based macromolecular model building with ISOLDE" (*Tristan Croll*) When: Saturday, 8/26, 14:15 - 15:00 pm Where: Room 214 Best wishes, Dorothee -- 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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Generation of residual electron density maps using IAS (inter atomic scatteres) model
by Ankur Kumar Singh 08 Aug '23

08 Aug '23

Dear Members, I am working on a protein structure resolved at 1.1 angstroms, and I am trying to generate a residual electron density map. I am following a series of articles from Prof. Afonine (Macromolecular refinement at subatomic resolution with interatomic scatterers<https://pubmed.ncbi.nlm.nih.gov/18007035/>). Here, an IAS modeling of the protein structure is done, followed by refinement in Phenix. The residual density is observed in conventional maps. I am trying to figure out how to create an IAS model for my protein structure. Please suggest any relevant method/article to obtain the model. And also, is it possible to have an IAS model for a protein resolved at 1.1 angstroms? Many thanks for considering my request. ----- Regards, Ankur K Singh Graduate Student

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General interest: Data matters session at the ACA 2023 in Baltimore
by John R Helliwell 05 Aug '23

05 Aug '23

Dear Colleagues, I have placed a note about this at the IUCr Committee on Data Public Forum: https://forums.iucr.org/viewtopic.php?f=39&t=457&sid=54ca94b6a4db968acc28ab… including a weblink to my slides at Zenodo. Best wishes, John Emeritus Professor John R Helliwell DSc

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[URGENT] Sorry: Fatal problems interpreting PDB file
by Esra A 03 Aug '23

03 Aug '23

Hello everyone, I am Esra Ayan. I would like to ask you about getting an error in Phenix: *Sorry: Fatal problems interpreting PDB file* *I followed the below command to resolve this issue:* 1. just running "phenix.ready_set MR.1.pdb" 2. then running "phenix.refine MR.1.updated.pdb MR.1.mtz MR.1.ligands.cif refinement.input.xray_data.r_free_flags.generate=True This way, i was able to solve the problem but still getting high Rwork and Rfree values. I still couldn't lower the values even though I tried many ways. What is your recommendation about this issue? i was wondering if I did a mistake by using Step 1 and Step 2 commands. You can find the reference pdb and mtz files in the attachment. Any help would be appreciated. Kind regards, Esra Ayan

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Postdoctoral position in drug discovery
by Harp, Joel M 03 Aug '23

03 Aug '23

Postdoctoral position in drug discovery An opening is available in the drug discovery laboratory of Dr. Stephen Fesik for a post-doc in the field of protein x-ray crystallography. Responsibilities will include protein production, fragment screening by NMR, and all aspects of x-ray crystallography including preparation of protein-ligand complexes, crystallization, home/synchrotron data collection, and structure determination. Additional experience in molecular biology including construct design, cloning, site-directed mutagenesis and modeling is a plus. The ideal candidate should be self-motivated and be able to communicate efficiently in a highly collaborative environment. Please send cv to jason.phan(a)Vanderbilt.Edu<mailto:[email protected]> The Vanderbilt campus is located in Nashville Tennessee. Also known as Music City, Nashville is a fast growing and dynamic environment with plenty of cultural attractions and opportunities for outdoor recreation.

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High Temperature Factors with TLS
by Thomas, Leonard M. 03 Aug '23

03 Aug '23

Hello All, A general questions though phenix.refine is being used for refinement. A student I am working with has a structure that was solved and initially refined using TLS and NCS parameters. They were given the structure to gain some experience in refinement and they have been asking me some questions, I was not involved in the initial work. While everything seems to be happy and the model is correct with good refinement statistics for the most part one thing that I am unsure of is some of the heavier atoms (Phosphate and Sulfer) have very high temperature factors when looking at individual residues or ligands. The temperature factors are at least twice as high as the lighter atoms they are associated with. I am at a loss to explain what is going on, I really have not used TLS refinement a lot so there is that. Resolution is about 2.5 angstroms with good completeness. Thoughts? Thank You in advance Len Thomas Leonard Thomas, Ph.D. Biomolecular Structure Core, Director Oklahoma COBRE in Structural Biology Price Family Foundation Institute of Structural Biology University of Oklahoma Department of Chemistry and Biochemistry 101 Stephenson Parkway Norman, OK 73019-5251 Office: (405)325-1126 lmthomas(a)ou.edu<mailto:[email protected]> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl

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Job Advert: Drug Discovery Project Research Scientist position, Francis Crick Institute, London, UK.
by David Briggs 01 Aug '23

01 Aug '23

Dear all, We have a position available at the Francis Crick Institute - please share with any soon-to-finish PhD students and postdocs who might be interested: We seek a talented, highly motivated and independent post-doctoral project research scientist to work on a project to design protein kinase C beta selective inhibitors for B cell malignancies. Work will be carried out in Neil McDonald's laboratory at the Francis Crick Institute, in collaboration with clinician-scientist Ingo Ringshausen at the University of Cambridge, and is funded by a Cancer Research Horizon Therapeutic Catalyst Award. The project will be funded for 18 months in the first instance, with the potential for extension depending on progress. The project will build upon prior work within our laboratory to characterise and develop new, selective kinase inhibitors. The work will involve both optimisation of existing inhibitors, and the parallel discovery of novel inhibitors using an XChem Fragment screening approach at Diamond Light Source. The Francis Crick Institute is situated in central London, and is the largest single-site biomedical research institute in Europe, with excellent provision for X-ray crystallography and medicinal chemistry to allow rapid characterisation and follow-up of any lead compounds. Prior experience with baculovirus protein expression and X-ray crystallography would be advantageous. Informal enquiries can be made to Professor Neil McDonald (neil.mcdonald(a)crick.ac.uk). Application Deadline: 1st Sept 2023. For more details about the role and the application process, please see: https://crick.wd3.myworkdayjobs.com/External/job/London/Postdoctoral-Projec… -- Dr David C. Briggs CSci MRSB (he/him) Principal Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK Working hours: Mon-Fri 0900-1700 == about.me/david_briggs<https://about.me/david_briggs> | OrcID<https://orcid.org/0000-0002-9793-7339> | Google Scholar <https://scholar.google.co.uk/citations?user=DRKG5KwAAAAJ> The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT

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