- phenixbb - phenix-online.org

real space refine and nonbonded_weight
by Cheung, Alan 25 Oct '19

25 Oct '19

Dear Developers A structure we refined back in 2017, using phenix.real_space_refine on a cryoEM map @ 3.7A (version 1.11.1–2575) produces a clashscore of ~8 but the exact same refinement run with the latest phenix (version 1.17.1) generates a clashscore of ~22. Our refinements with the latest version on other EM structures tend to generate pretty high clashscores too. I think i've tracked this down to the nonbonded_weight parameter, which defaults to 1000 in the older version, and to 100 in the latest version. At which version did the default change, and is there a reason for it? I couldn't find it in the changelog. Alan

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rosetta.run_tests crash
by wtempel 24 Oct '19

24 Oct '19

Hi, has anyone tried the combination of phenix-1.17 and rosetta-2019.40? Crashes in my hands, crash log attached. I may have modified the phenix installation by phenix.python -m pip install readline, in case it matters. Any suggestions appreciated. Many thanks in advance. Wolfram Tempel

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Yeast microtubule model
by Sebastiano Pasqualato 24 Oct '19

24 Oct '19

Dear all, I’m addressing to people working in the microtubule field. Has someone created, or knows where I could find, a pdb file of the yeast microtubule, or a portion of it? I’m interested in studying the contacts between subunits within the lattice. I know one could generate that using yeast tubulin dimers, but I don’t know exactly how. If someone has already done that and is willing to share it, that would be extremely helpful. Thanks a lot in advance, ciao, S PS: sorry for the cross posting to members of both bulletin boards. -- Sebastiano Pasqualato, PhD Biochemistry and Structural Biology Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990

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Phenix-RSR model fit issue in CS-Map
by pramod kumar 23 Oct '19

23 Oct '19

Dear Experts, I have a map generated through cryosparc (ab initio-reconstr and homo-refine at 3.7A* FSC and sharpened in Scipion and separately in EMAN2). I have build the initial pdb through BALBES which has perfect validation parameters and nice fitting in the map (with the mtz output) but the co-ordinates are shifted from the true origin of CS-map. I used phenix-RSR to fit and refine, but validation results remained too far to accept the model as good solution and also a small region entered in wrong nearyby densities. So far following independent and downstream approaches I have taken:- In phenix; dock in map, map to model, rigid body refine followed by real space refine (with both .map and converted .mtz), using only chain A-map boxing and model generation through NCS. I have tried chimera fit for entire assembly and also only one chain in boxed map and full map but still the validation remained far from acceptable values and a small region in wrong neighboring density. Please help. -- Best regards, Promod

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errors in rosetta.refine
by Bram mylemans 18 Oct '19

18 Oct '19

dear I am trying to run rosetta.refine but get an error. I am using the latest version of phenix (1.17-3644) and I have tried to versions of rosetta (3.10 release date 2 Oct 2018 and 3.11 release date 26 Sept 2019) If I run rosetta.run_tests with rosetta 3.10 I get the following error message: DEBUG dumping error message ERROR: Rosetta exited with status 139 stderr output: Segmentation fault (core dumped) If I run with rosetta 3.11 I get a different error message: DEBUG dumping error message ERROR: Rosetta exited with status 127 stderr output: /opt/rosetta_3.11_phenix/main/source/bin/rosetta_scripts.python.linuxgccrelease: error while loading shared libraries: libcifparse.so: cannot open shared object file: No such file or directory Are these version of rosetta and phenix compatible?

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Small Molecule Discovery RFP - Deadline is October 28th
by Nick DeHaan 17 Oct '19

17 Oct '19

Hi PhenixBB, I thought this group might be interested in an academic research support program that helps identify new active compounds based on protein structure. The award provides investigators, postdocs, or grad students with approximately 72 small molecules predicted by machine learning to bind to their protein of interest. A few awards also provide in-kind support (with a value of up to $20k) for the assay work. Applications take ~30 minutes to complete, and >300 awards will be given out this cycle. Proposals are due by October 28th. You can find out more here: Website: www.atomwise.com/aims <http://bit.ly/31rz1B4> Infographic: http://www.atomwise.com/wp-content/uploads/2019/10/AIMS-Infographic-Stats_F… <http://bit.ly/31jRa3O> Flyer: http://www.atomwise.com/wp-content/uploads/2019/10/Atomwise-AIMS-Awards-Fly… <http://bit.ly/31nkVAI> Please feel free to reach out to me with any questions! Best regards, 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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Job opening: Scientist-I (Structural Biology) at Frederick National Laboratory for Cancer Research
by Dhirendra K Simanshu 17 Oct '19

17 Oct '19

Hello everyone, The Frederick National Laboratory for Cancer Research is looking for a Scientist with experience in protein chemistry and structural biology. The candidate will join the structural biology group within the NCI RAS Initiative program and work on the 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 Leidos Biomedical Research, Inc. *Office/Courier*: 8560 Progress Drive, C1012, Frederick, MD 21701 *USPS mail*: Post Office Box B, ATRF-C1012, Frederick, MD 21702 Dhirendra.Simanshu(a)fnlcr.nih.gov <Dhirendra.Simanshu(a)nih.gov>

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high B Factor after real space refinement against a cryoEM map
by Keda Zhou 17 Oct '19

17 Oct '19

Dear all, I am trying to do the real space refinement for my model against a 5.0 angstrom cryoEM map. All parameters look pretty good except the B factor. The mean of the B factor is close to 400. I am just wondering whether the low resolution makes the B factor this high. Does anyone have any idea or suggestion on the high B factor during real space refinement? Is it possible to reduce it? What is the actual meaning of this B factor? Thanks in advance. cody

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Two tenure-track faculty openings at Univ. of Missouri Biochemistry
by Tanner, John J. 14 Oct '19

14 Oct '19

Dear Colleagues, My department has two tenure-track faculty openings. Review of applications will begin on November 15, 2019. Click the link below for more information. https://biochem.missouri.edu/open-positions/ John J. Tanner Professor of Biochemistry and Chemistry Associate Chair of Biochemistry Department of Biochemistry University of Missouri 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Email: tannerjj(a)missouri.edu<mailto:[email protected]> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A

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file location changed
by Cygler, Miroslaw 14 Oct '19

14 Oct '19

Hi, In order to allow synchronization of files on my mac with the cloud server I had to move all files used by Phenix to a new directory, including the main Phenix folder. How do I change the paths to these files in phenix so that they are accessible to the software? Phenix would not start without the main Phenix folder returned back to the old location. How do I rectify this as well? Thanks for your help, Mirek

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