- phenixbb - phenix-online.org

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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Software developer role at Diamond Light Source
by Hall, Dave (DLSLtd,RAL,LSCI) 25 Nov '19

25 Nov '19

Dear all We currently have a role for a software developer to work with the MX group at Diamond Light Source (www.diamond.ac.uk/mx<http://www.diamond.ac.uk/mx>). The successful candidate will work with scientific staff and software developers to enable experiments across the diverse suite of MX beamlines. For details of the role and how to apply see here https://vacancies.diamond.ac.uk/vacancy/data-acquisition-scientist-for-stru… Best regards Dave Hall MX Group Diamond Light Source -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Postdoc position in methods development at LBNL
by Dorothee Liebschner 22 Nov '19

22 Nov '19

Announcing a postdoc position on behalf of Dr. Kanupriya Pande: ======================================================================== Post-doc position in methods development in the Molecular Biophysics and Integrated Bioimaging division at LBL. The overall objectives of the project are to develop theory and computation to extract conformational heterogeneity and disorder from diffraction and imaging data. The position is available immediately with an initial appointment for 2 years with the possibility of renewal based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. Qualified candidates must have a PhD in Biophysics, Physics, Mathematics, Chemistry, or related fields. Job description and how to apply: https://lbl.referrals.selectminds.com/jobs/computational-biologist-postdoc-… ======================================================================== -- Project 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] weight optimization in refinement
by Alexei Gorelik 22 Nov '19

22 Nov '19

Thanks! What I meant is, phenix.refine seems to run a number of optimization threads (usually 10-14) independent of the number of cores specified (for example, 4 or 8). If i specify 8 cores, is there a way to force it to run 8 weight optimizations? On Nov 22, 2019 1:24 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: Hi Alexei, Is there a setting to control the number of parallel weight optimization threads in phenix.refine? nproc parameter controls number of CPUs to be used in weight optimization. Also, is there a way to force phenix.refine to perform global real-space refinement (rsrg)? No. There is some built-in logic, phenix.refine does it when these conditions are met and it can un-do the result if it is not an improvement. Is there particular need to do this in your context? Pavel

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problems running refinement of shaken model against half map
by L. Hielkema 22 Nov '19

22 Nov '19

Hi all, For the validation of my model to my map in phenix 1.17.1 I tried to refine my shaken model (0.5Å) against my half map in phenix real space refine. However, whatever I try I get a weird behaviour in the FSC(Model-map), see the image below. It seems not to be able to reach 0 in the correlation, but keeps getting stuck at 0.1. I tried various things to solve this, but unfortunately nothing helps: - Using the other half map - Cut of the heterogeneous part of my model and map and refine this - Used refined data without using a mask for the last iterations - Used different resolutions to refine against - Tried data from someone else in the lab (same microscope, same imaging conditions), to check if I am doing something wrong (this gave good results) When doing the same refinement in Refmac5 in ccpem 1.4 it does seem to work, however I would not like to switch programs, because this will mess up my final model. Best, Lisa

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weight optimization in refinement
by Alexei Gorelik 22 Nov '19

22 Nov '19

Hi, Is there a setting to control the number of parallel weight optimization threads in phenix.refine? Also, is there a way to force phenix.refine to perform global real-space refinement (rsrg)? Most of the time, when the "real-space" option is selected, it only carries out rotamer fitting (rsrl). I do know there's a separate real-space refinement program in Phenix. Thanks!

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Secondary structure restraints
by Luca Pellegrini 20 Nov '19

20 Nov '19

I have a protein-DNA complex and would like to apply SS restraints. What is the best way to apply the SS restraints to the protein only, using the GUI? I have tried the following: Select ‘Use secondary structure restraints’ in the ‘Refinement Settings’ tab ‘Select Atoms’ In the Selection Editor window, 'Find Secondary Structures' Removed manually all nucleic acid restraints in ‘Base Pairs’ and Stacking Pairs’ tabs Save and close. However, phenix refinement keeps switching SS restraints for nucleic acids to True. Kind regards, 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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Molybdenum cofactor refinement
by Cristiano Mota 20 Nov '19

20 Nov '19

Hi all, I'm using phenix.refine to refine a structure of a Molybo-protein at 1.9Å. The MGD cofactors (molybdopterin guanine dinucleotide) are being refined with a weird distorted geometry causing some clashes. The Fo-Fc maps show that something is going wrong in the aromatic rings interatomic distances. I'm using the readyset to pick up MGD and metal restraints. Am I using the right protocol? Best regards, Cristiano Mota -- *Cristiano de Sousa Mota* Postdoctoral Researcher, Macromolecular Crystallography Group UCIBIO / FCT - Universidade Nova de Lisboa 2829-516 Caparica, Portugal (00351 212948300, ext 10962) http://xtal.dq.fct.unl.pt/

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Deadline Extended to December 9th
by Nick DeHaan 20 Nov '19

20 Nov '19

Hi PhenixBB, Thanks for sharing information about the AIMS Awards with your colleagues! Many have told us they really appreciated it. We’ve had requests for more time - so we extended the deadline to December 9th! For anyone with a protein target of interest, the AIMS Award program can help you discover new molecular tools, start new drug development efforts, and get published. The program is open to investigators, postdocs, and graduate students worldwide. We encourage you to check out our flyer for more information: Flyer <http://bit.ly/37oIrS3> You can apply directly on the website: atomwise.com/aims. Please don't hesitate to reach out with any questions! Best, Nick Nick DeHaan, MsE *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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cryo-EM density modification
by Tom Terwilliger 19 Nov '19

19 Nov '19

Hi Phenix cryo-EM users, For those of you trying out density modification for cryo-EM (phenix.resolve_cryo_em), the automatic estimation of resolution in the current version uses unmasked resolution instead of masked, in some cases resulting in running density modification at too low a resolution. Consequently it is best with this version if you specify your nominal resolution. To run it you can type: phenix.resolve_cryo_em half_map_1.ccp4 half_map_2.ccp4 \ seq_file=seq.dat resolution=3.5 or something like that. It requires the current nightly build to run. You might also want to wait just a short while and a version that has this and a few other bugs fixed, a GUI, full documentation, and an example dataset will be out (hopefully this week). The full description of the method is at https://www.biorxiv.org/content/10.1101/845032v1 Let me know of any problems or suggestions! All the best, Tom T -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

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Differences in refinement statistics
by Chancievan Thangaratnarajah 19 Nov '19

19 Nov '19

Hello, I have noticed differences in the refinement statistics between two different Phenix versions (see attachments) even though I am using the same cryo-EM map and model as input. The most notable difference are rotamer outliers, which were 0 % in Phenix 1.16-3549 and now 6 % in Phenix 1.17-3660. I was wondering whether anyone has noticed a similar behaviour? Or is there something that I have missed? Best, Chancie.

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Error in sequence assignment
by Tom Terwilliger 18 Nov '19

18 Nov '19

Hi Nicholas, I'm afraid there isn't a way to say which sequence goes with which chain. I would suggest using the tool phenix.replace_side_chains. Give it 1 chain and 1 sequence and if they have the same length it should just put it in. If it doesn't work, try phenix.sequence_from_map which can do the same thing. Let me know if that doesn't do it! All the best, Tom T Date: Sun, 17 Nov 2019 17:07:16 -0500 From: Nicholas Gao <dominion146(a)GMAIL.COM> Subject: Specify chain assignment in sequence file for rebuild-in-place of phenix.autobuild Dear CCP4, I currently have an MR solution that has the wrong sequence. The pdb file of the solution contains 3 chains, and I'd like to use the rebuild-in-place functionality within phenix.autobuild to correct the sequence of all 3 chains. Phenix allows me to supply a sequence file as input for this job, it's not clear to me how I tell the program which sequence should be assigned to which chain. Anyone know how to do this? Sincerely, Nicholas Gao -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

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RapiData at SSRL 2020 - application deadline extended by one week!
by Smith, Clyde 15 Nov '19

15 Nov '19

Hi all, We have extended the deadline for applications for a place at the RapiData 2020 @ SSRL workshop to next Friday, November 22 2019! There are still a few spots left, so get your application in! The workshop will be held from March 30 - April 4 2020 on the SLAC campus in Menlo Park, California. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and 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). Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2020/ and use the links on the "registration" page to apply for the course. Successful applicants will be notified early in December 2019 and invited to register at that time. A limited amount of travel support funding may be available. We look forward to seeing you all out in sunny California in March 2020! Silvia Russi, Clyde Smith and Jeney Wierman (Organizers) srussi(a)slac.stanford.edu csmith(a)slac.stanford.edu jwierman(a)slac.stanford.edu

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General interest
by John R Helliwell 14 Nov '19

14 Nov '19

Dear Colleagues, I imagine the two articles that I describe in my posting at the IUCr’s Forum will be of interest to the MX community. See:- https://forums.iucr.org/viewtopic.php?f=39&t=427 All best wishes, John Emeritus Professor John R Helliwell DSc

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Scientist job position at AbbVie
by Longenecker, Kenton L 13 Nov '19

13 Nov '19

Hi - I'd like to draw attention of interested candidates to the following job opportunity with full description to apply at: http://abbvie.referrals.selectminds.com/jobs/senior-scientist-i-ii-protein-… Company overview: AbbVie (NYSE:ABBV) is a global, research-driven biopharmaceutical company committed to developing innovative advanced therapies for some of the world's most complex and critical conditions. The company's mission is to use its expertise, dedicated people and unique approach to innovation to markedly improve treatments across four primary therapeutic areas: immunology, oncology, virology and neuroscience. In more than 75 countries, AbbVie employees are working every day to advance health solutions for people around the world. Job Description: The Structural Biology Group at AbbVie Headquarters in Lake County, Illinois, USA is seeking a highly motivated scientist to join our Structure-Based Drug Discovery team. The ideal candidate should have extensive hands-on experience in modern structural biology techniques and computational methods of molecular structure analysis. As part of multidisciplinary teams, the Senior Scientist will utilize X-ray crystallography techniques to identify ligands and provide insight to advance drug discovery targets through structure-based design. The successful candidate will contribute to drug discovery projects across the portfolio of AbbVie interests that also include therapeutic antibodies and novel biologics. ________________________________ Kenton Longenecker, Ph.D. Sr. Principal Research Scientist AbbVie R&D Discovery, DDST Structural Biology 1 N. Waukegan Road, AP10-LL North Chicago, IL 60064 OFFICE 847-938-1428 EMAIL kenton.longenecker(a)abbvie.com<mailto:%[email protected]> abbvie.com<http://www.abbvie.com> This communication may contain information that is proprietary, confidential, or exempt from disclosure. If you are not the intended recipient, please note that any other dissemination, distribution, use or copying of this communication is strictly prohibited. Anyone who receives this message in error should notify the sender immediately by telephone or by return e-mail and delete it from his or her computer. ________________________________

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Submissions to the Computational Crystallography Newsletter – 30 NOV 19
by Nigel Moriarty 12 Nov '19

12 Nov '19

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission for the January 2020 issue is 30 November 2019. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.phenix-2Donline.org…>. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Postdoc Position in Berkeley
by Petrus Zwart 08 Nov '19

08 Nov '19

Dear All, We have two postdoc positions open in LBNL's Center for Advanced Mathematics in Energy Research Applications (CAMERA; https://www.camera.lbl.gov/) to work on a diverse set of problems in managing, cleaning and interpreting biophysical data ranging from microscopy to crystallography. https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=88805 https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=88480 Feel free to contact me for more information. Regards Peter Zwart -- ------------------------------------------------------------------------ P.H. Zwart Staff Scientist Molecular Biophysics and Integrated Bioimaging & Center for Advanced Mathematics for Energy Research Applications Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 PHENIX: http://www.phenix-online.org CAMERA: http://camera.lbl.gov/ -------------------------------------------------------------------------

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RapiData at SSRL 2020 reminder - just over a week left to apply!
by Smith, Clyde 04 Nov '19

04 Nov '19

Hi all, A reminder that there is only a week left to apply for a place at the RapiData 2020 @ SSRL workshop. Applications close the middle of this month, November 15 2019. The workshop will be held from March 30 - April 4 2020 on the SLAC campus in Menlo Park, California. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and 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). Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2020/ and use the links on the "registration" page to apply for the course. Successful applicants will be notified early in December 2019 and invited to register at that time. A limited amount of travel support funding may be available. We look forward to seeing you all out in sunny California in March 2020! Silvia Russi, Clyde Smith and Jeney Wierman (Organizers) srussi(a)slac.stanford.edu jwierman(a)slac.stanford.edu csmith(a)slac.stanford.edu

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