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Re: [phenixbb] Restricting real-space refinement and weights to specific atom selections
by Josh Cofsky 20 Oct '21

20 Oct '21

Thanks for that suggestion, Phil. After several weeks, I've finally found solid answers to all my questions, which I'll write here in case anyone reading this message is curious: Q1: Is there any way to apply different map weights to different pieces of the structure during refinement? A1: Pavel tells me the answer is no—this feature is not available in Phenix yet. The way I was able to accomplish something to a similar effect was by performing full-model refinements at different weights. Then, in a final refinement job, use torsion restraints from each of those output models (as reference models) across the desired stretches of residues. Clunky, but it solved a few problems for me. Q2: How is the generic "weight" parameter at the bottom of the Phenix GUI applied to the refinement? A2: The target function is T = Tmap * weight + Trestraints. At the time of writing this message, there is a typo in the Phenix Real-Space Refine documentation, which incorrectly reports the target function as "T = Tmap + weight * Trestraints" (Pavel confirmed). Q3: Why is the PDB validation telling me I have geometric issues that were not acknowledged by Phenix? A3: Phil is right. The ESD for several nucleic acid bond lengths and angles is wide as compared to the sigma tolerated by wwPDB. To fix this, I went into the CIF files within the geostd folder and made the following changes to the troublesome RNA and DNA nucleotide files: *data_AD.cif, data_TD.cif, data_CD.cif, data_GD.cif:* length: C1'-N1, ESD=0.020 C3'-O3', ESD=0.020 angles: O4'-C1'-N9/N1, ESD=0.30 *data_U.cif* angles: C5-C6-N1, ESD=0.5 C6-N1-C2, ESD=0.5 *data_C.cif* angles: C6-N1-C2, ESD=0.5 *data_A.cif* angles: N7-C8-N9, ESD=0.5 Best, Josh On Mon, Sep 13, 2021 at 7:23 AM Philip D. Jeffrey <pjeffrey(a)princeton.edu> wrote: > :: most of the outliers are not acknowledged as such (by Phenix), and I > only become > :: aware of them when the wwPDB validation tells me they are there. > > Check that the equilibrium values that PDB are using and the ones that > Phenix are using are the same. If they're not (or if the sigmas are way > different) you're not going to be able to change the outcome just by > changing weights. > > Phil Jeffrey > Princeton > > ------------------------------ > *From:* phenixbb-bounces(a)phenix-online.org < > phenixbb-bounces(a)phenix-online.org> on behalf of Josh Cofsky < > josh.cofsky(a)gmail.com> > *Sent:* Sunday, September 12, 2021 9:42 PM > *To:* phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org> > *Subject:* Re: [phenixbb] Restricting real-space refinement and weights > to specific atom selections > > I now realize that I am confused as to what the mentioned "weight" > parameter refers to. The Phenix RSR documentation contains a line that > reads "T = Tmap + weight * Trestraints"—if I'm understanding correctly > (?), this means a larger "weight" value should yield greater conformity to > geometric restraints at the expense of model/map fit. In reality, I observe > the opposite trend in my refinements (which is why I assumed it was a "map > weight"). Can someone clarify what "weight" (Refinement Settings > "Other > Options") refers to? > > The reason I am exploring these questions is that Phenix RSR is > introducing bond angle outliers into a low-resolution area of a DNA > molecule in my model—most of the outliers are not acknowledged as such (by > Phenix), and I only become aware of them when the wwPDB validation tells me > they are there. I assumed this was the result of overfitting to the map > because setting "weight" to 0.0 prevented these outliers from appearing, > but at the expense of map-model fit in the remainder of the structure > (which is why I wanted to apply different weights to different segments of > the model). > > Thanks, > Josh > > On Sun, Sep 12, 2021 at 12:21 PM Josh Cofsky <josh.cofsky(a)gmail.com> > wrote: > > Hi all, > > I'm using phenix.real_space_refine to refine a model into a cryo-EM map. > My local map resolution is highly variable across the molecule, and using a > single map weight (the parameter shown in the Refinement Settings > "Other > Options" in the GUI) on the whole model leads to poor map-to-model fit in > some locations and overfitting in others. Potential solutions could be to: > 1. assign different map weights to different segments of the model (based > on a user-specified atom selection) > OR > 2. perform iterative refinements with different weight settings, holding > different (user-specified) segments of the model fixed during each > iteration (I suspect this isn't possible based on Pavel's message here: > http://phenix-online.org/pipermail/phenixbb/2021-May/025037.html) > > Is either of these approaches (or another one that accomplishes the same > goal) possible? I am using the Phenix GUI, but if this is only possible in > command line, and you're willing to share an example command that > accomplishes either of these tasks, please let me know. > > Thanks! > -Josh > > (also, apologies if this is a duplicate message...still trying to figure > out the phenixbb listserv) > >

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Job opening: Scientist/Sr. Scientist, Structural Biology at Plexxikon Inc, South San Francisco, CA, USA
by Ying Zhang 16 Oct '21

16 Oct '21

Dear all, This post is to bring your attention to a job opportunity of a scientist/Sr. Sicentist position at Plexxikon Inc. We are looking for a highly motivated, structural biologist with expertise in crystallography. Plexxikon (https://www.plexxikon.com/) is located in South San Francisco at CA, USA. We only consider candidates based in US. This Scientist will be a critical member of the Structural Chemistry team. This is an exceptional opportunity to gain experience in structure-guided drug discovery in a successful biotech company. Plexxikon utilizes its proprietary discovery platform to successfully develop a portfolio of competitively differentiated clinical and preclinical stage compounds in a number of therapeutic areas, including two marketed drug. Zelboraf(tm) (vemurafenib) was the first precision medicine to be approved for the treatment of BRAF-mutant metastatic melanoma; Turalio(tm) (pexidartinib) was the first FDA-approved therapy for tenosynovial giant cell tumor. You can find details about this position at https://careers.jobscore.com/careers/plexxikon/jobs/scientist-structural-bi… Please apply through the link. Best Regards, Ying Zhang, Ph.D Sr Director, Research Planning Plexxikon Inc

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missing statistics for rama-z
by Hannah Bridges 16 Oct '21

16 Oct '21

Hello, I have a PDB for which, when I run either realspace refinement or validation, phenix does not show rama-z scores for helix or sheet (and the structure is not entirely loops..) Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.08), residues: 8101 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.50 (0.06), residues: 8101 It seems peculiar to this one model, as other very similar ones are fine, but is this something that other people have seen before? I can supply the PBD off-list for investigation. Best wishes Hannah -- Dr Hannah Bridges Investigator Scientist MRC Mitochondrial Biology Unit The Keith Peters Building University of Cambridge Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY United Kingdom Telephone : 01223 252812

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Nightly build downloads
by Armando Albert 02 Oct '21

02 Oct '21

Dear all, I am unable to find the nightly build releases from the Phenix web page. Is there any issue I do not know? Armando

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Phenix website change complete
by Dorothee Liebschner 01 Oct '21

01 Oct '21

Hi everyone, We changed the website. Let us know if there are any issues. Best wishes, The Phenix Team -- 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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Phenix website maintenance on 9/30/2021
by Dorothee Liebschner 30 Sep '21

30 Sep '21

Hi everyone, The Phenix website will be changed tomorrow, Thursday 9/30/2021. Therefore, the website might not be available for a couple of hours. If you encounter any problems after the switch - which we will announce on the BB - please let us know. We will change the urls of some pages due to some reorganization, but the addresses of the most visited pages should be the same, such as download, documentation and so on. Best wishes, The Phenix Team -- 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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problems with phenix.refine and wwPDB deposition
by Błażej Bagiński 24 Sep '21

24 Sep '21

Dear fellow Phenix bulletin boarders, I'd like to ask for help with refinement-deposition file conflict. I 'finished' solving the structure (protein, 1 chain, 2 ligands), doing the final refinement in phenix.refine. Structure looks okay and does not report any errors in phenix/coot. I than started the deposition with the wwPDB OneDep System.After long check, my files were rejected (multiple errors, with the best one being "coordinates not found"). Following the FAQ, I run the prepare_pdb_deposition, but the results were the same. I also tried using PDB_Extract (https://pdb-extract.wwpdb.org/), with its result file also generating plethora of errors. As a control, I put the same phenix.refine file into the PDB-REDO server, and its results finished wwPDB validation successfully. Trouble is, PDB-REDO is quite aggressive and messed up one ligand, occupancies and two loops, so I would prefer to not submit it for anyone to see. How do you make refinement output compatible with wwPDB? Is there a way to run PDB-REDO without the REDO? Kind regards, Blazej Baginski

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Download issues
by Billy Poon 24 Sep '21

24 Sep '21

Hi everyone, If you are having download issues, can you post a message here? We are seeing reports of download issues from some users and we want to determine how widespread the issue is. Some users have said that the download works after waiting for a bit or by using the incognito or private mode of their browser. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

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Postdoctoral Research Opportunity in Cryo-EM at University of Washington, in Seattle, USA
by George Wisedchaisri 18 Sep '21

18 Sep '21

Hi, I have a job opening announcement for a joint postdoctoral position in the Catterall and Zheng Labs at University of Washington, in Seattle, WA, USA. Please see the link below for more detailed info. http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20210913/9614f6ba/att… Thanks, George Wisedchaisri -- *Postdoctoral Research Position* *Senior Fellow or Instructor Appointment Level* *Structural Basis for Function and Pharmacology of Voltage Gated Sodium and Calcium Channels* *Laboratories of William A. Catterall and Ning Zheng* *Department of Pharmacology, University of Washington, Seattle, WA 98195-7280 USA* *Please respond by e-mail to wcattlab(a)uw.edu <wcattlab(a)uw.edu> with Postdoctoral Application on the Subject Line* *Position Requirements* PhD or equivalent in biochemistry, biophysics, bioengineering, or structural biology. Experience in molecular biology, cell culture, and protein expression, purification, and characterization. Excellent communication skills and successful experience in a team research environment. Two years experience with cryo-EM data collection, processing, and analysis. Successful determination of a protein structure by cryo-EM. *Application Requirements* Curriculum Vitae Names of three referees *University of Washington is an affirmative action, equal opportunity employer. All qualified applicants will receive consideration without regard to race, color, religion, sex, sexual orientation, gender identity, gender expression, national origin, age, protected veteran or disabled status, or genetic information.* -- George Wisedchaisri, Ph.D. Research Assistant Professor of Pharmacology --------------------------------------------- University of Washington School of Medicine Department of Pharmacology 1959 NE Pacific St Seattle, WA 98195-7280

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Today is the last day to register for the SSRL/LCLS User Meeting
by Mooers, Blaine H.M. (HSC) 18 Sep '21

18 Sep '21

Dear Phenixbb: Today is the last day to register for the SSRL/LCLS User Meeting that starts on Monday. It is free and virtual. https://events.bizzabo.com/SLAC-UsersMeeting-2021/home. The poster session runs 12 - 1 PM Pacific Time M-Th. You use the gathertown software to attend it. Navigation of the poster session is like playing a 1990s computer game. I was on the poster judging team. We spent this week judging the posters virtually. We made our selections of the seven poster prize finalists today. All of the semifinalist posters were excellent. Best regards, Blaine SSRL UEC member and past chair. Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine Director of the Laboratory of Biomolecular Structure and Function Academic Director, Biomolecular Structure Core, COBRE in Structural Biology Full Member, Cancer Biology Program, Stephenson Cancer Center University of Oklahoma Health Sciences Center Mailing Address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Struc… COBRE in Structural Biology: https://www.ou.edu/structuralbiology

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(no subject)
by Smita Yadav 17 Sep '21

17 Sep '21

Dear All, hello to everyone. I wanted to know which gromac version is mostly used for simulation in linux. -- With Regards Smita Yadav

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NIH-funded Postdoc, Membrane Protein Structural Biology (Nebraska, USA)
by Alex Vecchio 14 Sep '21

14 Sep '21

Dear Phenix Community, I would like to bring your attention to an NIH-funded Postdoc position in the Vecchio Lab <https://vecchio-lab.unl.edu> at the University of Nebraska studying membrane proteins and membrane protein assemblies using X-ray crystallography and cryoEM. We are looking for a recent or soon-to-be Ph.D., with experience in membrane proteins and one structural technique. Potential exists for the candidate to *acquire cryoEM expertise* during the postdoc training via a recently well-scored NSF fellowship. For more information, please read our ad HERE <https://jobrxiv.org/job/vecchio-lab-at-university-of-nebraska-27778-postdoc…> . To apply or for specific questions, please contact me at avecchio(a)unl.edu. All the best, Alex -------------------------------------------- Alex J. Vecchio, Ph.D. *Assistant Professor* University of Nebraska–Lincoln Department of Biochemistry Center for Integrated Biomolecular Communication 1901 Vine Street N113 / N114 Beadle Center [Lab / Office] Lincoln, NE 68588 avecchio(a)unl.edu 1 [402] 472-2933

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Assistant Researcher Senior Position in the KU Protein Structure Laboratory
by Lovell, Scott W 14 Sep '21

14 Sep '21

The Protein Structure and X-ray Crystallography Laboratory (PSXL) at the University of Kansas (KU) is seeking a full-time Assistant Researcher Senior to work on a variety of structural biology projects. As a core laboratory, the PSXL collaborates with multiple investigators to obtain structures of their proteins of interest using X-ray crystallography and delivers dozens of structures annually. Additionally, the PSXL is involved in NIAID funded R01 grants and manages the structural biology efforts for projects aimed at antiviral inhibitor development. As such, this position will involve structural biology work to facilitate the structure-guided development of inhibitors targeting the MERS-CoV and SARS-CoV-2 main proteases. For a full description of the position and to apply, GO TO: https://employment.ku.edu/staff/20030BR Regards, Scott __________________________________________________ Scott Lovell Ph.D., Director Protein Structure and X-Ray Crystallography Laboratory University of Kansas Del Shankel Structural Biology Center 2034 Becker Drive Lawrence, KS 66047 Office: SBC 1015 email: swlovell(a)ku.edu<mailto:[email protected]> phone: 785-864-3772 fax: 785-864-8141 https://psxl.ku.edu/ __________________________________________________

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Restricting real-space refinement and weights to specific atom selections
by Josh Cofsky 13 Sep '21

13 Sep '21

Hi all, I'm using phenix.real_space_refine to refine a model into a cryo-EM map. My local map resolution is highly variable across the molecule, and using a single map weight (the parameter shown in the Refinement Settings > "Other Options" in the GUI) on the whole model leads to poor map-to-model fit in some locations and overfitting in others. Potential solutions could be to: 1. assign different map weights to different segments of the model (based on a user-specified atom selection) OR 2. perform iterative refinements with different weight settings, holding different (user-specified) segments of the model fixed during each iteration (I suspect this isn't possible based on Pavel's message here: http://phenix-online.org/pipermail/phenixbb/2021-May/025037.html) Is either of these approaches (or another one that accomplishes the same goal) possible? I am using the Phenix GUI, but if this is only possible in command line, and you're willing to share an example command that accomplishes either of these tasks, please let me know. Thanks! -Josh (also, apologies if this is a duplicate message...still trying to figure out the phenixbb listserv)

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Extending a structure
by E Artikis 10 Sep '21

10 Sep '21

I have a pdb with a fibril composed of three identical chains. I'd like to expand the fibril from three to 15 chains. Is there a way to do this? It's essentially a copy/paste action, but I can't figure it out. Thanks!

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Phenix opens COOT but does not load map or model
by Boniecki, Michal 08 Sep '21

08 Sep '21

Hello, I used to be able (with previous phenix versions) load models into COOT after refinement. Now when I click open in COOT, only COOT window is open but neither maps or model are loaded.Also there is no "connected to phenix' displayed in COOT sidebar I have no problems with loading and displaying both in phenix or pymol (open with phenix or open with pymol buttons). Any suggestions how to solve it would be appreciated. COOT 0.9.5, phenix 1.19.2-4158 Michal

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Job posting: Scientist (crystallography) at Frederick National Laboratory for Cancer Research
by Dhirendra K Simanshu 08 Sep '21

08 Sep '21

Hello everyone, The Frederick National Laboratory for Cancer Research is looking for a Scientist with experience in protein chemistry and structural biology (crystallography). The candidate will join the structural biology group within the NCI RAS Initiative program and work on the protein-protein and protein-small molecule complexes. For detailed information and to apply for this position, please use this link: https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leido… Best regards Dhirendra Simanshu -- Dhirendra Simanshu Principal Scientist, Team Lead - RAS Structural Biology NCI RAS Initiative Frederick National Laboratory for Cancer Research 8560 Progress Drive, C1012, Frederick, MD 21701 Dhirendra.Simanshu(a)fnlcr.nih.gov <Dhirendra.Simanshu(a)nih.gov>

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IUCr’s Committee on Data recent meeting minutes now online
by John R Helliwell 06 Sep '21

06 Sep '21

Dear Colleagues, I imagine that you will be interested in the IUCr’s Committee on Data recent meeting minutes which are now online here:- https://forums.iucr.org/viewtopic.php?f=39&t=441 Best wishes, John Emeritus Professor John R Helliwell DSc Chairman IUCr Committee on Data

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copy R-free array from reference mtz using command line?
by Aaron Thompson 31 Aug '21

31 Aug '21

PhenixBB, I know this can be done via GUI, but is it possible to copy the R-free array from a reference mtz to a new mtz using the command line? I don’t see this as an option in phenix.reflection_file_converter. Thank you, Aaron

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NORA workshop on AlphaFold2 and RoseTTAFold, 31 August and 1 September
by Randy John Read 27 Aug '21

27 Aug '21

Hi, I’ve just learned that this online workshop is generally open, not just to members of the Norwegian Artificial Intelligence Consortium (NORA), and it’s free! Information, including the current programme and a link to registration, can be found here: https://www.nora.ai/events/AlphaFoldv2.0-and-RoseTTAFold-workshop%20.html I’ll be talking a bit about experiences with models from AlphaFold2 and RoseTTAFold, but the real draw should be talks by people who really understand these two deep learning algorithms: Minkyung Baek (first author on the RoseTTAFold paper, from David Baker’s group) and a representative of the DeepMind team that developed the two versions of AlphaFold. Sameer Velankar will also be there to talk about the exciting new AlphaFold database at the EBI. Best wishes, Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Re: [phenixbb] NORA workshop on AlphaFold2 and RoseTTAFold, 31 August and 1 September
by Randy John Read 27 Aug '21

27 Aug '21

9 am CEST (Norway). Pretty early for our North American colleagues, especially those on the west coast! > On 27 Aug 2021, at 05:18, Robert Rose <rbrose2(a)ncsu.edu> wrote: > > Does the workshop start on August 31 at 9 am GMT? > > On Thu, Aug 26, 2021 at 2:27 PM Randy John Read <rjr27(a)cam.ac.uk> wrote: > Hi, > > I’ve just learned that this online workshop is generally open, not just to members of the Norwegian Artificial Intelligence Consortium (NORA), and it’s free! Information, including the current programme and a link to registration, can be found here: > > https://www.nora.ai/events/AlphaFoldv2.0-and-RoseTTAFold-workshop%20.html > > I’ll be talking a bit about experiences with models from AlphaFold2 and RoseTTAFold, but the real draw should be talks by people who really understand these two deep learning algorithms: Minkyung Baek (first author on the RoseTTAFold paper, from David Baker’s group) and a representative of the DeepMind team that developed the two versions of AlphaFold. Sameer Velankar will also be there to talk about the exciting new AlphaFold database at the EBI. > > Best wishes, > > Randy Read > > ----- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > The Keith Peters Building Fax: +44 1223 336827 > Hills Road E-mail: rjr27(a)cam.ac.uk > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Peptide bond to symmetry related molecule
by Damian Ekiert 24 Aug '21

24 Aug '21

Hi All, We are refining several structures in which the N-terminal residue of chain A appears to form a peptide bond to the C-terminal residue of its symmetry mate, chain A. In reality, the target protein consists of 4 identical helical repeats that pack end to end. Slippage and averaging over the 4 possible registers leads to the appearance of an infinitely long polymer in the crystal, with no breaks between protomers. Is it possible to enforce a peptide bond to symmetry mates in Phenix, and what is the easiest way to do this? I have found a several cases in the archives on how to deal with symmetry clashes, but struggling to figure out how to deal with a peptide bond. Thanks for your help! Best, Damian - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damian Ekiert Assistant Professor Skirball Institute | NYU School of Medicine Depts. Cell Biology and Microbiology damian.ekiert(a)ekiertlab.org www.bhabhaekiertlab.org

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Postdoctoral position in Computational Biochemistry
by Yasser Almeida 23 Aug '21

23 Aug '21

Dear all, The group of Computational Biochemistry of Prof. Elsa Sánchez-García at the University of Duisburg-Essen is announcing a Postdoc position focused on the computational design of chemical tools and inhibitors for the study of proteins and protein-protein interactions involved in cell state transition. The deadline for applications has been changed to September 30th. More information can be found at https://www.uni-due.de/computational-biochemistry. Best regards, Yasser -- Dr. Yasser Almeida-Hernandez Postdoctoral Researcher Computational Biochemistry group T01 R03 D45 Faculty of Biology University of Duisburg-Essen Universitätsstr. 2, 45117 Essen Email: yasser.almeida-hernandez(a)uni-due.de <%20yasser.almeida-hernandez(a)uni-due.de> Phone: +49 201 183 2457

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Project Scientist and Postdoctoral research positions in XFEL, ML, and material science computational methods
by Aaron Brewster 18 Aug '21

18 Aug '21

Hello, I'm excited to announce that two positions are immediately open in my group in the fields of material science, serial X-ray crystallography, and machine learning. Links to postings: Computational Project Scientist - https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=93507 Computational Postdoctoral Scholar - https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=93506 In these exciting roles, you will work in the Molecular Biophysics and Integrated Bioimaging Division on a project that will research adding advanced spatial and symmetry aware neural network training methods to small-molecule chemical crystallography and material science data processing. This will use AI methods developed as part of a close collaboration between teams at Lawrence Berkeley National Labs (LBNL), University of Connecticut, and MIT. The larger group is researching crystal engineering of hybrid coordination polymers towards achieving rational control over the optoelectronic properties of low-dimensional nanostructures. These positions are focused on the chemical crystallography aspect of the program, but the successful candidates will be expected to participate in all aspects of the program, including data collection at X-ray free electron lasers worldwide, data analysis on supercomputing facilities, structure solution, research on AI driven structure prediction, paper writing, and software management. Both roles are 3 year appointments. This work will be part of the Department of Energy Integrated Computational and Data Infrastructure for Science <https://insidehpc.com/2021/08/doe-funds-15m-for-integrated-computational-an…> Research program. Specific details follow. Berkeley Lab is committed to Inclusion, Diversity, Equity and Accountability (IDEA) <https://diversity.lbl.gov/ideaberkeleylab/> and strives to continue building community with these shared values and commitments. Berkeley Lab is an Equal Opportunity and Affirmative Action Employer. We heartily welcome applications from women, minorities, veterans, and all who would contribute to the Lab’s mission of leading scientific discovery, inclusion, and professionalism. In support of our diverse global community, all qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. *Computational Project Scientist* *What You Will Do:* - Design and train neural networks that allow determination of the unit cell and crystal orientations of small molecule crystals from sparse, randomly oriented diffraction patterns. This will involve curating training sets from simulated datasets and from existing and new experimental data that will be collected. - Research methods to scale training and use of these neural networks on multiple nodes in high performance computing environments. - Lead data collection and processing at X-ray free electron sources. - Maintain a detailed record of work performed. - Document and manage code developed using standard source control methods. - Publish in peer-reviewed journals. - Present research at seminars and conferences. - Assist Principal Investigator in developing grant proposals. - Document and maintain existing and new data processing software, including the cctbx build system. *What is Required:* - 2-5 years of relevant experience beyond the highest degree in Physics, Statistics, Crystallography, Artificial Intelligence, or a related field. - A strong background in Python, C++, or an equivalent platform for scientific computing. - A track record of critical thinking, problem solving, and mathematical intuition, demonstrated through publications and presentations. *Desired Qualifications:* - Familiarity with general Python scientific data packages such as NumPy, SciPy, and pandas. - Versed in modern coding practices for scientific computing, including algorithm design and evaluation, source code management under a revision control system like git, and incorporation of readable documentation and comments. - Expertise in computational approaches in at least one of the areas related to the research is required, including but not limited to small-molecular crystallography, structure solution and refinement, unit cell determination, neural network design, training, and evaluation, high speed computing, image analysis, large dataset analysis, graph theory, error propagation and statistics, signal processing, and GPU acceleration. - Familiarity with small-molecule material design and synthesis. - Strong analytical and organizational skills. - Excellent interpersonal, oral, and written communication skills. - Ability to work independently as well as part of a diverse team. *Computational **Postdoctoral Scholar* *What You Will Do:* - Design and train neural networks to model diffraction from small molecule crystals. This will involve curating training sets from simulated datasets and from existing and new experimental data that will be collected. - Assist in data collection and processing at X-ray free electron sources. - Maintain a detailed record of work performed. - Document and manage code developed using standard source control methods. - Publish in peer-reviewed journals. - Present research at seminars and conferences. * What is Required:* - PhD degree in Physics, Statistics, Crystallography, Artificial Intelligence, or a related field. - Experience in computational approaches in at least one of the areas related to the research, including but not limited to small-molecular crystallography, structure solution and refinement, unit cell determination, neural network design, training, and evaluation, high speed computing, image analysis, large dataset analysis, graph theory, error propagation and statistics, signal processing, and GPU acceleration. - Strong analytical and organizational skills. - Excellent interpersonal, oral, and written communication skills. - Ability to work independently as well as part of a diverse team. * Desired Qualifications:* - Familiarity with Python, C++, and general scientific data packages such as NumPy, SciPy, and pandas. - Familiarity with small-molecule material design and synthesis. Please do not hesitate to reach out to me for more information. Thank you, Aaron S. Brewster, PhD Computational Research Scientist, Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720

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Specifying import-time dependencies in _ext libraries?
by Russell M. Taylor II 18 Aug '21

18 Aug '21

I've developed an mmtbx_probe_ext module that makes use of objects defined in iotbx_pdb. I've added that library to LIBS= in the SConscript file, and it is able to link and run properly. However, when a Python script imports mmtbx_probe_ext, that load fails unless the same script has previously imported from iotbx: The following works: from iotbx.map_model_manager import map_model_manager import mmtbx_probe_ext as probe But the following fails: import mmtbx_probe_ext as probe from iotbx.map_model_manager import map_model_manager ImportError: /home/taylorr/rlab/cctbx-reduce-python27/build/lib/mmtbx_probe_ext.so: undefined symbol: _ZNK5iotbx3pdb9hierarchy5chain5atomsEi How do I tell Sconscript (or what do I do in my _bpl file) to tell Python that it needs to load the other module first? Thanks, Russ Taylor --- Russell M. Taylor II, Ph.D. russ(a)reliasolve.com taylor(a)redbudlabs.com rtaylor(a)aqueti.com russ(a)outloveracism.org www.cs.unc.edu/~taylorr

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