July 2018 - phenixbb - phenix-online.org

high level python API
by wtempel 06 Jul '18

06 Jul '18

Hi, I would like to call programs like phenix.refine from a python script. Is the python subprocess module my best bet? Or does phenix provide its own interface similar to, say, ccp4 dispatchers? Thanks. Wolfram Tempel

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Re: [phenixbb] [cctbxbb] Deprecating legacy support (CentOS 5, Windows 32-bit) in CCTBX and Phenix
by Billy Poon 06 Jul '18

06 Jul '18

Hi Luc, No worries, let us know of any other concerns. Thanks! -- 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 On Fri, Jul 6, 2018 at 2:22 AM Luc Bourhis <luc_j_bourhis(a)mac.com> wrote: > Hi Billy, > > > Or do you need something sooner? > > No, considering the timeframe for the move to conda is before the end of > the year. I just wanted to know so that I can start advertising the change > to the people on my side. Sorry if I missed that point during the meeting > you invited me on. > > Best wishes, > > Luc > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

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Invitation to International conference "BIOMEMBRANES 2018"
by Marin, Egor 06 Jul '18

06 Jul '18

Fellow structural biologists, we are pleased to invite you to participate in the 4th biannual international C*onference* “BIOMEMBRANES 2018”, which will be held on October 1-5, 2018 at the Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia. This is the first meeting within the International Conference Series “Virtual Human – Imaging Across Scales” co-organized by scientists from Russia, Germany, China, and USA. Our speakers will focus on cutting-edge problems of modern integrative structural biology of biomembranes and membrane proteins, theoretical biophysics of membrane systems and computer modelling. The conference will highlight the role of biomembranes in aging and age-related diseases such as cancer, neurodegenerative (Alzheimer’s, Parkinson’s) and cardiovascular diseases. The talks will be given by world-leading scientists from Russia, USA, Germany, France, the Netherlands, China, Spain, Italy, Sweden and Switzerland. Preliminary scientific program, as well as the up-to-date list of speakers please find here: https://biomembranes2018.ru/program/ In parallel, an international *School* “Mechanisms of aging and age-related diseases” will take place as a satellite event of the Conference on September 30 - October 5, 2018. The full information about the school will soon be available on our web-site https://biomembranes2018.ru/sa tellite-events. Early bird registration until 31.07, registration until 14.09. Further information is available on the conference web site http://biomembranes2018.ru. We are looking forward to meet you in Dolgoprudny! sincerely yours, Organizing Committee

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Re: [phenixbb] [cctbxbb] Deprecating legacy support (CentOS 5, Windows 32-bit) in CCTBX and Phenix
by Billy Poon 06 Jul '18

06 Jul '18

Hi Luc, With the planned migration to conda for dependencies, the idea is to build one linux installer using the compilers in conda (currently GCC 7.2, https://conda.io/docs/user-guide/tasks/build-packages/compiler-tools.html) and then test that installer on multiple distributions of linux. CentOS 7 would be one of the distributions used for testing. Or do you need something sooner? We currently do not build our installers on CentOS 7, but I have checked that the CentOS 6 installer runs and that the regression tests (phenix_regression.test_all_parallel, which is a superset of cctbx regression tests) pass on CentOS 7. -- 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 On Wed, Jul 4, 2018 at 7:31 AM Luc Bourhis <luc_j_bourhis(a)mac.com> wrote: > Hi Billy, > > > The upcoming Phenix 1.14 official release will still have installers for > CentOS 5 and Windows 32-bit, but since CentOS is no longer supporting > CentOS 5, and RedHat is only supporting RHEL5 through their Extended Life > Cycle Support Add-On (until November 30, 2020), we are planning on > deprecating CentOS 5 support (32-bit and 64-bit). In addition, we are > planning on deprecating 32-bit support for Windows because only a few > percent (< 5% for both Windows and CentOS 5) of our Phenix downloads are > for 32-bit versions. > > > If you deprecate CentOS 5, will you start to support CentOS 7? I mean > right now, nightly tests run CentOS 5 & 6. Do you plan to make it 6 & 7? I > am asking so that I can start planning for Bruker among other things… > > Best wishes, > > Luc > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

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Deprecating legacy support (CentOS 5, Windows 32-bit) in CCTBX and Phenix
by Billy Poon 02 Jul '18

02 Jul '18

Hi everyone, The upcoming Phenix 1.14 official release will still have installers for CentOS 5 and Windows 32-bit, but since CentOS is no longer supporting CentOS 5, and RedHat is only supporting RHEL5 through their Extended Life Cycle Support Add-On (until November 30, 2020), we are planning on deprecating CentOS 5 support (32-bit and 64-bit). In addition, we are planning on deprecating 32-bit support for Windows because only a few percent (< 5% for both Windows and CentOS 5) of our Phenix downloads are for 32-bit versions. Please let us know if support for CentOS 5 (32-bit and/or 64-bit) or 32-bit Windows is a requirement for your systems. If so, also please describe your setup. Thanks! -- 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

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