October 2021 - phenixbb - phenix-online.org

RapiData 2020 applications open
by Smith, Clyde 15 Nov '21

15 Nov '21

Applications are now open for the 2020 edition of RapiData at SSRL. RapiData is a practical course in macromolecular X-ray diffraction data collection, data processing and structure solution. The aim of the RapiData course is to educate and train young scientists in data collection and processing methods at synchrotron beamlines, using state-of-the-art software and instrumentation. The course will be held in sunny California at the Stanford Synchrotron Radiation Lightsource (SSRL) located on the SLAC National Accelerator Laboratory campus in Menlo Park, CA, from March 30 - April 4 2020. Course organizers for 2020 are Silvia Russi, Clyde Smith and Jeney Wierman. 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 and small angle scattering). Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2020/ and use the links on the "registration" page to apply for the course. The application deadline is November 10 2019. Successful applicants will be notified shortly thereafter, and invited to register and book accommodation at the SLAC Guesthouse at that time. A limited amount of travel support funding may be available. Please direct questions to Silvia Russi (srussi(a)slac.stanford.edu), Jeney Wierman (jwierman(a)slac.stanford.edu) or Clyde Smith (csmith(a)slac.stanford.edu).

1 2

Phenix 1.20 release candidates
by Billy Poon 02 Nov '21

02 Nov '21

Hi everyone, We are doing a final Python 2.7 release of Phenix and the first release candidate is available from https://phenix-online.org/download/nightly_builds.cgi This release will contain several new features, such as tools for using AlphaFold models. The release after that is planned to be in Python 3.7. 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

1 2

Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 27 Oct '21

27 Oct '21

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 11 DEC 2021. Please consider writing an article of general interest to the community. 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 is attached to this email. 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 ORCID : orcid.org/0000-0001-8857-9464

1 0

Re: [phenixbb] Restricting real-space refinement and weights to specific atom selections
by Josh Cofsky 19 Oct '21

19 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) > >

1 0

Job opening: Scientist/Sr. Scientist, Structural Biology at Plexxikon Inc, South San Francisco, CA, USA
by Ying Zhang 15 Oct '21

15 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

1 0

missing statistics for rama-z
by Hannah Bridges 15 Oct '21

15 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

3 3

Nightly build downloads
by Armando Albert 01 Oct '21

01 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

4 3

Phenix website change complete
by Dorothee Liebschner 30 Sep '21

30 Sep '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

1 0