- phenixbb - phenix-online.org

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

Phenix website maintenance on 9/30/2021
by Dorothee Liebschner 29 Sep '21

29 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

1 0

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

3 2

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

1 1

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

1 0

Today is the last day to register for the SSRL/LCLS User Meeting
by Mooers, Blaine H.M. (HSC) 17 Sep '21

17 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

1 0

(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

2 1

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

1 0