- phenixbb - phenix-online.org

Problem getting Phenix and Rosetta working together
by Dale Tronrud 01 Feb '13

01 Feb '13

Hi, I would like to get mr_rosetta running on my CentOS 6.3 64 bit computer but I can't seem to get them connected. I'm probably doing something stupid/silly but I'm stumped. I've downloaded, installed and compiled rosetta3.4 in the folder /usr/local/rosetta3.4. There are a bunch of files in rosetta_source/bin and they are executable. However, typing the following commands shows my problem. [dale@athena tln]$ echo $PHENIX_ROSETTA_PATH /usr/local/rosetta3.4 [dale@athena tln]$ ls -l $PHENIX_ROSETTA_PATH total 156 drwxr-xr-x. 10 root root 4096 Mar 20 2012 Antibody drwxr-xr-x. 3 root root 4096 Jul 26 2011 foldit-3.4 -rw-r--r--. 1 root root 1115 Mar 25 2012 new_apps.note drwxr-xr-x. 25 root root 4096 Mar 20 2012 protocol_capture -rw-r--r--. 1 root root 460 Mar 25 2012 README.Copyrights -rw-r--r--. 1 root root 12 Mar 25 2012 README.version -rw-r--r--. 1 root root 3345 Mar 25 2012 release.note drwxr-xr-x. 19 root root 106496 Mar 25 2012 rosetta3.4_user_guide drwxr-xr-x. 9 root root 4096 Mar 25 2012 rosetta_database drwxr-xr-x. 61 root root 4096 Mar 20 2012 rosetta_demos drwxr-xr-x. 11 root root 4096 Jan 30 15:27 rosetta_source drwxr-xr-x. 7 root root 4096 Mar 27 2012 rosetta_tests drwxr-xr-x. 13 root root 4096 Mar 20 2012 rosetta_tools [dale@athena tln]$ phenix_regression.wizards.test_command_line_rosetta_quick Skipping phenix rosetta tests: rosetta build not available. I can try "mr_rosetta" itself but it just tells me that I need to set PHENIX_ROSETTA_PATH. What, in particular, is Phenix looking for to determine that Rosetta is installed? Dale Tronrud

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Seats are still available for RapiData - the deadline is in 4 days for our course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 01 Feb '13

01 Feb '13

We will present RapiData 2013, the fifteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 21-26 April 2013: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the eleventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 21 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Photon Sciences and Biology Dept Mail Stop, Bldg 463 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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dzp
by Fumiaki Yumoto 31 Jan '13

31 Jan '13

Sent by iPhone

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January 2013 Computational Crystallography Newsletter
by Nigel Moriarty 31 Jan '13

31 Jan '13

Folks The latest edition of the Computational Crystallography Newsletter is available at http://phenix-online.org/newsletter The table of contents is listed below. Articles cctbx tools for transparent parallel job execution in Python. I. Foundations cctbx tools for transparent parallel job execution in Python. II. Convenience functions for the impatient. Short communications Phenix / MolProbity Hydrogen Parameter Update PSI SBKB Technology Portal: A Web Resource for Structural Biologists Fitting tips #5 - What’s with water FAQ - I'm seeing a lot of CIF files. Are they all restraints? Cheers Nigel -- Nigel W. Moriarty, PhD Building 64R0246B, Physical Biosciences Division 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

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Hirshfeld (rigid bond) test
by amakal＠chem.uw.edu.pl 31 Jan '13

31 Jan '13

Good Morning, I have a question concering ADP-s analysis and validation. Thanks to the recent discussion on this list I learned about the tools for general ADP-s statistics and average B-factor plotting in PHENIX. Has anyone ever tried to similarly document/visualize the values of the Hirshfeld's rigid bond test for macromolecules, using phenix/cctbx tools? I know the Hirshfeld's can be calculated during phenix refinement (there is this rigid_bond_test keyword), but I would like to analyze the values for the final model... With regards, Anna Makal

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phenix.refine command line
by Simon Kolstoe 30 Jan '13

30 Jan '13

Hi guys, I'm just trying to install phenix on a students new macbook pro running OS10.8.2, and want to get phenix.refine working on the command line. I've put in: alias setphenix="source /Applications/PHENIX-1.8.1-1168/Contents/phenix-1.8.1-1168/phenix_env.sh" in the .bashrc which seems to execute OK (and already pointed the .bash_profile to .bashrc) however whenever I then type phenix.refine I get command not found. As this is the same setup that I have running on my own machine I am a bit confused as to what is happening! Thanks! Simon

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Phaser with fixed solution
by Ursula Schulze-Gahmen 30 Jan '13

30 Jan '13

I am trying to solve a structure by molecular replacement in phaser using 2 model fragments. I think I may have placed the 1st fragment correctly. I don't quite understand how to best proceed with a fixed ensemble searching for the second fragment in phaser-MR. If I select "use partial solution from previous job", do I still need to read in the coordinates of that previous solution for one ensemble? And If I do, should I read in the starting coordinates or the placed output from this 1st molecular replacement? The second question is about how to relax the restraints fr the packing. In the "other settings" sub window is a section for packing. Could someone explain to me what the different options in this packing section mean? Which of them should I change to allow for more close contacts? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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2013 workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 30 Jan '13

30 Jan '13

Fourth Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 24 - June 28, 2013 Application deadline: April 22, 2013 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologist to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome. However the course organization may not be able to offer travel or accommodation support. The number of participants will be limited to 15. There is no registration fees for all selected participants. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (for graduate students only; 1/2 to 1 page), should be sent electronically to meilleurf(a)ornl.gov<mailto:[email protected]> before April 22, 2013. Detailed information can be found on the course web page: http://neutrons.ornl.gov/conf/gcnb2012/ (gcnb2013 in construction). Best Regards, Flora Meilleur, Ph. D Assistant Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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Re: [phenixbb] Unable to install phenix 1.8.1-1168 on Scientific Linux 6.3 64 bits
by Engin Ozkan 29 Jan '13

29 Jan '13

I just installed yesterday the latest nightly build on our Scientific Linux 6 (6.3, I believe) machine using the 64-bit FC3 installer. No problems. Engin Engin Özkan Garcia Lab, Stanford -------- Original message -------- From: Nathaniel Echols <nechols(a)lbl.gov> Date: To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Subject: Re: [phenixbb] Unable to install phenix 1.8.1-1168 on Scientific Linux 6.3 64 bits On Fri, Jan 25, 2013 at 4:15 PM, Davi de Miranda Fonseca <davi.fonseca(a)ntnu.no> wrote: > I installed Scientific Linux 6.3 64 bits, updated everything and installed a > couple of things that I think would be necessary. Then I uncompressed > phenix-installer-1.8.1-1168-intel-linux-2.6-x86_64-fc3.tar to /tmp and tried > to install, however I got some errors. Hence, I installed a couple more > things and tried installing again. The first thing to try when something like this happens is to download one of the other 64-bit installers. In most cases the fc3 build is preferred, but there are some newer distributions where an installer built on a more recent version of Fedora is preferable. I would start with fc8 and work your way up. The second thing to try, if all of the binary installers fail, is to install from source. > ***** And here are the last lines of > /tmp/phenix-installer-1.8.1-1168/build-binary/intel-linux-2.6-x86_64/scientifix/log/binary.log: >... > /usr/local/phenix-1.8.1-1168/build/intel-linux-2.6-x86_64/base/bin/python: > /lib64/libc.so.6: version `GLIBC_2.14' not found (required by > /usr/local/phenix-1.8.1-1168/build/intel-linux-2.6-x86_64/base/bin/python) > > By the way, Scientific linux 6.3 comes with glibc 2.12. To be honest I simply don't understand library versioning issues - the Fedora 3 machine we build that installer on currently has glibc 2.3, so I don't know where the GLIBC_2.14 is coming from. I think it will be significantly more work to figure out a workaround than trying the other installers, though. Unfortunately we do not actually have a Scientific Linux system here - the closest I could find was CentOS 6.2, and that works okay. -Nat _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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Re: [phenixbb] phenix.refine command line
by Nathaniel Echols 29 Jan '13

29 Jan '13

(a reminder: you *must* send messages to the list from the exact email address you subscribed with - if not it will reject the posting, even if the actual server is the same. this happens at least once a week...) In any case the .profile solution sounds correct to me, although I still can't remember what the difference between all of the different login scripts is. ---------- Forwarded message ---------- From: "Lenin Domínguez" <acheron24(a)gmail.com> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Cc: Date: Tue, 29 Jan 2013 10:07:07 -0600 Subject: Re: [phenixbb] phenix.refine command line This is the way I have enabled phenix via command line: source /Applications/PHENIX-dev-1269/Contents/phenix-dev-1269/phenix_env.sh This line is located in my .profile. This works fine for me. Best regards. On Tue, Jan 29, 2013 at 9:16 AM, Simon Kolstoe <s.kolstoe(a)ucl.ac.uk> wrote: > > yes! > > On 29 Jan 2013, at 14:55, R.D. Oeffner wrote: > > > Hi Simon, > > > > Just to be clear; did you actually exectute the alias command before attempting to run phenix.refine? > > > > rob > > > > > > On Jan 29 2013, Simon Kolstoe wrote: > > > >> Hi guys, > >> > >> I'm just trying to install phenix on a students new macbook pro running OS10.8.2, and want to get phenix.refine working on the command line. I've put in: > >> > >> alias setphenix="source /Applications/PHENIX-1.8.1-1168/Contents/phenix-1.8.1-1168/phenix_env.sh" > >> > >> in the .bashrc which seems to execute OK (and already pointed the .bash_profile to .bashrc) however whenever I then type phenix.refine I get command not found. As this is the same setup that I have running on my own machine I am a bit confused as to what is happening! > >> > >> Thanks! > >> > >> Simon > >> > >> > >> _______________________________________________ > >> phenixbb mailing list > >> phenixbb(a)phenix-online.org > >> http://phenix-online.org/mailman/listinfo/phenixbb > >> > > > > -- > > Robert Oeffner, Ph.D. > > Research Associate, The Read Group > > Department of Haematology, University of Cambridge > > Cambridge Institute of Medical Research > > Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY > > www-structmed.cimr.cam.ac.uk, tel:01223763234, mobile:07712 887162 > > > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb -- Lenin Domínguez-Ramírez Los enemigos fortalecen. Los aliados debilitan. Os digo esto confiando que comprendáis por qué actúo como actúo sabiendo a ciencia cierta que en mi Imperio se acumulan grandes fuerzas con un único deseo: el de destruirme. Quizá vosotros que leéis estas palabras conozcáis bien lo que ocurrió realmente, pero dudo que lleguéis a comprenderlo. - Leto II

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