- phenixbb - phenix-online.org

Emergency power test at Berkeley this weekend (12/13-12/16)
by Billy Poon 13 Dec '19

13 Dec '19

Hi everyone, To mitigate disruptions from future power shut offs due to wildfire concerns, we are performing an emergency power test for our web servers. This will affect the phenix-online.org and cci.lbl.gov servers. The websites, mailing lists, and repositories will remain available, but the servers will be running on emergency power instead. The servers will be switched to emergency power at around 2 pm Pacific time on Friday (12/13) and switched back to main power around 10 am Pacific time on Monday (12/16). Please let me know if you experience 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 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Re: [phenixbb] map to model fsc did not start from 1
by BuddySphinx 11 Dec '19

11 Dec '19

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map to model fsc did not start from 1
by Yangqi Gu 11 Dec '19

11 Dec '19

Dear Phenix developer, I have a question regarding the map to model fsc. I have a filament map and a model with arbitrary copy of the protomer ( I built them in Chimera), then I used the filament model to refine against my map. But I encountered an issue is that the reported FSC (map to model) did not start from 1 but rather 0.8. I am wondering if there is anyway to fix it. Also, in the case of a filament, how do I use NCS operator to refine rather than manual building the filament model? I tried specifying NCS with helical symmetry, but it did not work. Best, Yangqi

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Re: [phenixbb] problems running refinement of shaken model against half map
by L. Hielkema 06 Dec '19

06 Dec '19

Dear Pavel, Thanks again for your answer. I understand that you have some concerns with regard to the validation we use. Now this makes me really curious how the rest of the EM community feels about this. > "widely used" does not always mean "makes sense". As it often happens, some may just blindly follow the crowd. And how "widely" it is used, in fact? I stated my arguments as to why this does not make sense (to me at least). I'm yet to hear any strong counter-arguments. > So you stated the following before: "First off, I think this way of validation is quite faulty conceptually... How you know 0.5A is the best number and say not 0.7 or 0.3? By shaking the model, you validate the shaken (perturbed) model, which is not the model you are publishing and reporting statistics for. If you shake the model twice with same shake doze, you will get two different models with the same amount of perturbation, which means numbers you derive from such models can (and likely will) be different.” Is there anyone that would have any strong counter arguments? Or thinks along the same way? Because we would really like to know if we should change anything in our approach. Or would then the approach that Pavel suggest with the phenix tool Comprehensive validation be a good solution to this issue? > The paper you refer to indeed describes the protocol they followed but it does not answer concerns that I raised before. > > History knows plenty of examples of something being almost a standard for a while and then discarded later. Such as cutting off low-resolution diffraction data (because at the time there was no good bulk-solvent models invented) or cutting data by 2 or 3 "sigma" criteria (because maximum-likelihood target functions were not in use yet), etc etc etc. Or not adding H atoms to atomic models... > > Cryo-EM isn't as mature as protein crystallography where most procedures and protocols are pretty much standard. Cross validation for cryo-EM is yet to settle to some more meaningful method. There is indeed a number of attempts made so far but none of them seem to be as good as Brunger's free-R approach! Sure many things have to be still established, but it would be nice to know what is the generally accepted method at the moment according to the community. > >> As far as I could see the phenix tool Comprehensive validation did not provide the validation against the half maps, that one needs to obtain FSCwork and FSCfree, which is described in the attached papers. > > This is correct, it doesn't for reasons I mentioned before. Best, Lisa > On 5 Dec 2019, at 21:02, Pavel Afonine <pafonine(a)lbl.gov> wrote: > > Hi Lisa, > >> Thanks for your answer. Though I am a bit confused, as far as I and my group understand this method is widely used for several years (see attached papers for first introduction and since then you see many performing this type of validation). > > "widely used" does not always mean "makes sense". As it often happens, some may just blindly follow the crowd. And how "widely" it is used, in fact? I stated my arguments as to why this does not make sense (to me at least). I'm yet to hear any strong counter-arguments. > > The paper you refer to indeed describes the protocol they followed but it does not answer concerns that I raised before. > > History knows plenty of examples of something being almost a standard for a while and then discarded later. Such as cutting off low-resolution diffraction data (because at the time there was no good bulk-solvent models invented) or cutting data by 2 or 3 "sigma" criteria (because maximum-likelihood target functions were not in use yet), etc etc etc. Or not adding H atoms to atomic models... > > Cryo-EM isn't as mature as protein crystallography where most procedures and protocols are pretty much standard. Cross validation for cryo-EM is yet to settle to some more meaningful method. There is indeed a number of attempts made so far but none of them seem to be as good as Brunger's free-R approach! > >> As far as I could see the phenix tool Comprehensive validation did not provide the validation against the half maps, that one needs to obtain FSCwork and FSCfree, which is described in the attached papers. > > This is correct, it doesn't for reasons I mentioned before. > > All the best, > Pavel >

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Submission deadline on Monday
by Nick DeHaan 05 Dec '19

05 Dec '19

Hi PhenixBB, The extended deadline for the AIMS Awards program is less than a week away! If any PIs, postdocs, or grad students you know are interested in submitting a proposal, please remind them to apply on the website by Monday, December 9th. Website: www.atomwise.com/aims <http://bit.ly/2PkkOlB> Best regards, Nick Nick DeHaan *Partnering Executive* *Atomwise* <http://www.atomwise.com/> | *Better Medicines Faster* ᐧ -- Confidentiality Notice: The information contained herein is for informational purposes only. This message is private and the information contained in this message, including any attachments, contains information that may be confidential, privileged and/or proprietary. It is intended to be read only by the individual or entity to whom it is addressed. If you are not the intended recipient, please notify the sender by replying to this message, delete the material immediately from your system and note that you must not review, disclose, copy, distribute or take any action in reliance on or in reference to this message, including any attachments. No confidentiality, privilege, or property rights are waived or lost by any errors in transmission. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.

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15 PhD scholarships in Braunschweig, Germany
by Blankenfeldt, Wulf 29 Nov '19

29 Nov '19

Dear colleagues & prospective Ph.D. students, The Technische Universität Braunschweig in collaboration with Helmholtz Centre for Infection Research and Ostfalia University of Applied Sciences currently initiate the doctoral program "Drug Discovery and Cheminformatics for New Anti-Infectives (iCA)" which is granted by the Ministry of Science and Culture of Lower Saxony. The program aims at studying fundamental principles of drug discovery by combining life sciences and digital sciences. The iCA consortium is offering 15 Georg-Christoph-Lichtenberg scholarships (duration: 3 years). The program of the iCA consortium offers an ambitious, structured and interdisciplinary training based on top-level fundamental research. This joint program provides an internationally competitive research environment with state-of-the-art facilities. The participating groups use a variety of different methods, including experimental, digital, and theoretical approaches. More information about specific projects and participating groups can be found at: https://www.tu-braunschweig.de/en/pharmchem/translate-to-english-promotions… The graduate program starts in the period from February to July 2020. For details and individual project descriptions please refer to the scholarship announcement attached. If you have any questions, please contact pvz-apply(a)tu-braunschweig.de<mailto:[email protected]>. The program is open for applications now. Applications should include letter of motivation, curriculum vitae, certificates, etc. combined in a single PDF file (max. 15 MB). Please send your application to pvz-apply(a)tu-braunschweig.de<mailto:[email protected]> until 31 December, 2019. Please forward these information to interested colleagues. Kind regards, Wulf Blankenfeldt ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Silke Tannapfel Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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Position at Diamond: XChem Beamline Scientist
by Frank Von Delft 29 Nov '19

29 Nov '19

Dear all, We are recruiting as permanent position a Beamline Scientist on the XChem fragment screening facility at Diamond. This role is to join the XChem team to support academic and industrial users with experiments and service work, co-manage the XChem lab, develop new fragment-related methodologies, and over next few years, work on expanding the XChem offering beyond hit identification. If you are a technically-minded crystallographer that enjoys teaching or training people, like an organised life, thrive on collaboration and like to see how you're making others productive, you will enjoy this job. Besides, Diamond is incredibly collegial and has a terrific user community. The ad is here: https://vacancies.diamond.ac.uk/vacancy/xchem-beamline-scientist-404499.html (for some reason you may need to click twice on the link to make it work). The application deadline is the 15th Dec 2019, and we wil linterview on 17th Dec (i.e. before Xmas). If you have questions, contact me or Alice Douangamath <Alice.Douangamath(a)diamond.ac.uk><mailto:[email protected]>, who heads the facility. Frank -- Frank von Delft Professor for Structural Chemical Biology Principal Beamline Scientist: I04-1 Diamond Light Source +44 1235 778997 (office: M,T,T) +44 7471 026103 (mobile) Principal Investigator: Protein Crystallography Structural Genomics Consortium Oxford University +44 1865 617583 (office: W,F)

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Re: [phenixbb] Real space refine of long side chains
by Leonid Sazanov 27 Nov '19

27 Nov '19

Hi, We have addressed exactly this problem by writing a script, in which B-factors are refined first and only then real-space refinement happens. This allows disordered side-chains to acquire high B-factors and so they are not pulled into backbone anymore. This cycle is repeated twice to achieve convergence. Parameters for B-factor refinement (ADP restrains) were optimized to account for consistent lack of density for acidic side chains in cryoEM. It is described in: https://www.ncbi.nlm.nih.gov/pubmed/31492636 If needed, I can send a script. Best Leonid -- Prof. Leonid Sazanov FRS IST Austria Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: sazanov(a)ist.ac.at Date: Mon, 25 Nov 2019 19:11:16 +0000 From: Luca Pellegrini <lp212(a)cam.ac.uk> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Subject: [phenixbb] Real space refine of long side chains Message-ID: <37F0D7B2-3C9E-4FE1-B0BF-6B23F0D8925B(a)cam.ac.uk> Content-Type: text/plain; charset=us-ascii I have noticed that real-space refinement in cryoEM maps has a tendency to pull long disordered side chains (Lys, Glu etc) back towards main chain density, resulting in unrealistic hairpin-like bent conformations. Is there a way to counter or moderate this behaviour? It would save me from having to manually straighten them all out again afterwards... Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom lp212(a)cam.ac.uk tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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Group ADP refinement restraints
by Taylor Stevens 26 Nov '19

26 Nov '19

Hello, I am currently refining a low-ish resolution structure (through the phenix.refine GUI) with phenix version 1.14 and had some questions about the use of restraints in group ADP refinement. In the phenix.refine documentation (https://www.phenix-online.org/documentation/reference/refinement.html#refin… <https://www.phenix-online.org/documentation/reference/refinement.html#refin…>) it is stated that “Group isotropic ADP or TLS refinement do not use any restraints”, however, this does not seem to be the case. If I look in the log file I can see the following lines of text which I believe indicate that the restraints are being applied: |-group b-factor refinement (macro cycle = 0; iterations = 0)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = None | |——————————————————————————————————————| |-group b-factor refinement (macro cycle = 1; iterations = 22)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = 821.871| |——————————————————————————————————————| |-group b-factor refinement (macro cycle = 2; iterations = 22)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = 821.871| |——————————————————————————————————————| |-group b-factor refinement (macro cycle = 3; iterations = 22)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = 821.871| |——————————————————————————————————————| If I manually set the wu parameter to 0 under “Refinement target weights" nothing changes, however, if I navigate to "All parameters > ADP settings > Group B-Factors" in the GUI there is a “Use restraints” box that is checked by default. If I uncheck this box, there are no longer any restraints being applied according to the log file, and in the case of the structure I am refining, there is a substantial drop in the rfree/rwork. Is this an issue with the program or documentation? Or am I misunderstanding how the program is supposed to work? Is it generally a good idea to use group ADP refinement without restraints? Thanks, Taylor

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Real space refine of long side chains
by Luca Pellegrini 25 Nov '19

25 Nov '19

I have noticed that real-space refinement in cryoEM maps has a tendency to pull long disordered side chains (Lys, Glu etc) back towards main chain density, resulting in unrealistic hairpin-like bent conformations. Is there a way to counter or moderate this behaviour? It would save me from having to manually straighten them all out again afterwards... Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom lp212(a)cam.ac.uk tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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