- phenixbb - phenix-online.org

Postdoctoral position at the Drug Discovery Institute at Purdue University
by John M Hausman 17 Dec '18

17 Dec '18

Dear All: A position is available for a highly qualified and motivated postdoc with a strong background in Molecular/Cell Biology or Immunology. The successful applicant will be responsible for conducting research aimed at identifying and characterizing new drug targets for treatment of important human diseases. Activities may involve i) expressing and characterizing proteins that are upregulated in various disease states, ii) cloning, mutating, expressing and developing assays for studying functional aspects of the target proteins, iii) immunofluorescent staining of tissue sections from diseased tissues, iv) shRNA knockdown of desired proteins in cultured cells, and v) immunoblotting and other common biochemical assays. Management of day-to-day research goals and priorities, supervision of graduate students assigned to the same project, and mentoring of other research personnel regarding the design and execution of specific research methods/approaches may also be required. The lab is directed by Professor Philip S. Low in the new Drug Discovery Institute on the West Lafayette Campus of Purdue University. Other members of the lab are involved in designing new therapies for cancer, fibrotic diseases, infectious diseases, sickle cell disease, bone fractures and related pathologies, and autoimmune diseases, etc. Participation in some of these existing projects may also be required. Please send CV and list of three names of potential referees to: Philip S. Low Presidential Scholar for Drug Discovery Ralph C. Corley Distinguished Professor Department of Chemistry Purdue University 720 Clinic Dr. West Lafayette, IN 47907 Email: plow(a)purdue.edu<mailto:[email protected]> ________________________________

1 0

Help with AutoBuild
by Parthasarathy Sampathkumar 16 Dec '18

16 Dec '18

Dear All, These days my research often involves structure determination of the Antigen:Fab complexes, wherein the antigen structure is already known. Given this: (1). I would like to run AutoBuild in such a way that the program does not to touch antigen model, but only Re-builds only the Fab molecule; and (2). in some cases, due to structural-symmetry within the variable and constant domains of heavy- and light- chains, AutoBuild is searching and applying NCS operator while it is not present, and would like to avoid the same. How could these be done either in GUI or in command-line?!! Many Thanks in advance, Best Wishes Partha PS: Of course, when the data is at "high-enough resolution", I build Fab model manually after MR and Refinement. But, in the above case, resolution is only 3-ish angstrom.

2 1

speeding up effective resolution calculation
by Eric Williams 07 Dec '18

07 Dec '18

Greetings, all. I have what may be a naive question. :) I'm using phenix.resolution to calculate effective resolution, and I'm looking for ways to speed it up. I've tried a few different machine configurations, and it always takes around 20 minutes per structure. This is problematic for me, because I'm trying to collect data from the entire PDB. Does anyone here have experience using NumPy to optimize scripts and helpful suggestions for this case? Alternatively, how much speedup am I likely to get by rewriting the script in C and using it as a module? Thanks. :) Eric

3 2

New PDB archive reference paper now in NAR 2019 Database issue
by John Berrisford 05 Dec '18

05 Dec '18

An important <https://doi.org/10.1093/nar/gky949> new publication describing the activities and development of the Protein Data Bank (PDB), and authored by the whole wwPDB consortium, has been recently released in the 2019 Database issue of Nucleic Acids Research. Please see the following news release from the <https://www.wwpdb.org/news/news?year=2018#5c05780d3675962a10fcf7a9> wwPDB website: " <https://doi.org/10.1093/nar/gky949> Protein Data Bank: the single global archive for 3D macromolecular structure data has been published in the 2019 Database issue of Nucleic Acids Research. The paper was authored by "wwPDB Consortium" to underscore the importance of the global wwPDB partnership in managing the PDB archive. This article describes the development of the PDB under the stewardship of wwPDB, such as new archival content, master format and dictionary and major remediation efforts. The publication also emphasizes the importance of continued community interactions, the scientific and technical challenges the PDB faces, and charts the road ahead." -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 <http://www.pdbe.org/> http://www.pdbe.org <http://www.facebook.com/proteindatabank> http://www.facebook.com/proteindatabank <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

1 0

Re: [phenixbb] Molprobity values on output pdb
by Christopher Williams 30 Nov '18

30 Nov '18

Hi Boaz, Is it possible for you to send me (and just me, not the bulletin board) your file for testing? Thank you, if so. Alternatively, you can try using our alternate site at http:// altmolprobity .biochem.duke.edu, where a bugfix that probably addresses this issue is currently under testing. Thanks and good luck, -Christopher Williams ---Richardson Lab, Duke University On Fri, Nov 30, 2018 at 11:57 AM Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > Hi, > > > I noticed small differences between the molprobity > all-atoms clashscore reported in the output pdb file and the results > reported by the molprobity run (build 3318). > > > Cheers, > > > Boaz > > > > > > > > > > > > > *Boaz Shaanan, Ph.D. Dept. of Life > Sciences Ben-Gurion University of the > Negev Beer-Sheva > 84105 > Israel > E-mail: > bshaanan(a)bgu.ac.il <bshaanan(a)bgu.ac.il> Phone: 972-8-647-2220 > Fax: 972-8-647-2992 or 972-8-646-1710 * > > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

1 0

Validation Completeness Issue
by Antoine Koehl 29 Nov '18

29 Nov '18

Hi, I’m in the process of uploading data to the PDB. While AIMLESS had estimated my completeness at 94% (similar to the XTriage value of 93.2%), the internal PDB validation through EDS estimates my completeness to be closer to 83.5%. This is a rather large difference. Both are using the exact same resolution range (49.57-4.00). Is there something that EDS does differently for estimating completeness? Please advise, Antoine

2 1

Test message
by Billy Poon 28 Nov '18

28 Nov '18

This is just a test. -- 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

1 0

Alternate conformer clash problem in phenix.refine
by Aaron Oakley 20 Nov '18

20 Nov '18

Salve! I am refining a protein/ligand complex where the ligand is bound with two conformers. Conformer A is covalently bound to a cysteine residue. Conformer B is free. I have prepared an appropriate cif dictionary for the ligand including info on handling the link. The problem is that during refinement, non-bonded interactions between the two conformers appear to not be switched off and their geometry becomes distorted. Is this diagnosis correct? If so, is there a way to manually switch off interactions? With thanks, a++ Aaron Oakley Associate Professor School of Chemistry and Molecular Bioscience | Molecular Horizons | Faculty of Science, Medicine and Health University of Wollongong NSW 2522 Australia T +61 2 4221 4347 | F +61 2 4221 4287 [cid:[email protected]]

3 2

exclude clashes for non-symmetry contacts
by Edwin Pozharski 17 Nov '18

17 Nov '18

Is there some way to make phenix.refine to ignore clashes for specific pair(s) of chains? I am dealing with a rare case of twinning where same protein molecule exists in two orientations in the same unit cell. I tried just to duplicate the molecule and set initial occupancy to 0.5, but refinement fails (as I expected) saying that there are too many close contacts. Ideally, I would like to proceed with ignoring close contacts between, say, chains A/B. I am aware that one can exclude groups of residues from symmetry clashes, but these two copies are in the same cell. I guess I could try shifting one into the next unit cell and then excluding symmetry clashes, but even assuming that will work it is a rather ugly hack. The alternative is probably to define the second orientation as an alternative conformation. Aside from aesthetic objections, I don't want to lose the ability to restrain NCS - I need two orientations to be identical structures, and I am not sure yet whether I can use NCS groups defined via alternative conformers. Cheers, Ed.

2 4

Normalized B-factor
by Mehmet Sen 16 Nov '18

16 Nov '18

Hello, I used the Structural Comparison tool to obtain normalized B- factor values for a couple of models, each with multiple chains. Is there an efficient way to visualize the normalized B-factor values (by writing over the old B-factor values) for the models, preferably in PyMOL? Thanks, Joyce V.

2 1