- phenixbb - phenix-online.org

Phaser annoyance
by Morten Groftehauge 05 Feb '13

05 Feb '13

Hi guys, The pop-up warning from Phaser about lack of eLLG for the resolution of the data would be more informative if you added the value of eLLG so one wouldn't have to scroll back in the log to find it. It would also allow the user to see with a glance whether the warning is because eLLG is under 120 or under 60. And it seems like the 'non-simple' Phaser GUI is broken in 1.8.2-1288. At least I haven't been able to open it, neither from the main window or by opening a previous job (Ubuntu 10.04). Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

2 2

AUTOBUILD: sequence file for multiple chains
by Gino Cingolani 03 Feb '13

03 Feb '13

Hi All, my model contains multiple chains and I would like Autobuild to build them all. What is the correct way to give multiple sequences (in FASTA format) to Autobuild? In my 'seq.dat' file, shall I leave one (or two) spaces in between one sequence and the other? Thanks, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Terwilliger, Thomas C [terwilliger(a)lanl.gov] Sent: Saturday, February 02, 2013 9:55 PM To: PHENIX user mailing list Subject: Re: [phenixbb] autosol MIR with more than one native? Hi Ed, Unfortunately, autosol only has a way to deal with one native, so you'd need to average them together or run 2 runs, one with each. All the best, Tom T ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Edward A. Berry [BerryE(a)upstate.edu] Sent: Saturday, February 02, 2013 10:39 AM To: PHENIX user mailing list Subject: [phenixbb] autosol MIR with more than one native? Is it possible to run phenix.autosol MIR problem with two "native" datasets? And does this make sense, or would it be better to scale the two natives together to make a single dataset before running autosol? eab _______________________________________________ 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

2 2

autosol MIR with more than one native?
by Edward A. Berry 03 Feb '13

03 Feb '13

Is it possible to run phenix.autosol MIR problem with two "native" datasets? And does this make sense, or would it be better to scale the two natives together to make a single dataset before running autosol? eab

2 5

Re: [phenixbb] Problem getting Phenix and Rosetta working together
by Nathaniel Echols 01 Feb '13

01 Feb '13

---------- Forwarded message ---------- From: Dale Tronrud <dale(a)daletronrud.com> To: phenixbb(a)phenix-online.org Cc: Date: Fri, 01 Feb 2013 08:24:53 -0800 Subject: Re: [phenixbb] Problem getting Phenix and Rosetta working together Hi Tom, I was right! The source of the problem was in the stupid/silly category. I had left the "export" out. I didn't notice the problem since my test scripts didn't include the "-f" option, like yours, so they were reading the init scripts every time. Thanks for pointing me to your scripts so I could figure this out. Dale Tronrud On 1/31/2013 2:11 PM, Terwilliger, Thomas C wrote: > > Hi Dale, > > I think the check that is giving you the error is: > > if (! $?PHENIX_ROSETTA_PATH) then > echo "Skipping phenix rosetta tests: rosetta build not available." > goto skip > > This is located in > > $PHENIX/phenix-dev-1117/phenix_regression/wizards/test_command_line_rosetta_quick.csh > > I'm puzzled how that can give you the error message you are getting unless the environment is different in the script you are running from your shell, but maybe now with the location of this file you can track it down? > > All the best, > Tom T > > > On Jan 31, 2013, at 3:01 PM, Dale Tronrud wrote: > >> Hi, >> >> I would like to get mr_rosetta running on my CentOS 6.3 64 bit >> computer but I can't seem to get them connected. I'm probably >> doing something stupid/silly but I'm stumped. >> >> I've downloaded, installed and compiled rosetta3.4 in the folder >> /usr/local/rosetta3.4. There are a bunch of files in rosetta_source/bin >> and they are executable. However, typing the following commands >> shows my problem. >> >> [dale@athena tln]$ 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 >> _______________________________________________ >> 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 >

1 0

MR: Apply rotation and translation to structure factors
by Shweta Kailasan 01 Feb '13

01 Feb '13

Hello, I am trying to use a cryo-EM map as a MR model for an Xtal data set. I have calculated structure factors for my map using SFALL. And also used rotcross and trans.com (from AMORE) to determine best possible rotation and translation solutions. Is there is a program/script available that can be used to apply those rotations and translation to structure factors ? Most programs start with a coordinate file (pdb) as a model whereas my initial model is a map. I tried to use Phaser but it didnot work out. Any help would be highly appreciated. Thank you. -S <peter.ramsumair(a)credit-suisse.com>

2 1

Problem getting Phenix and Rosetta working together
by Dale Tronrud 31 Jan '13

31 Jan '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

4 3

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 31 Jan '13

31 Jan '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) =========================================================================

1 0

dzp
by Fumiaki Yumoto 31 Jan '13

31 Jan '13

Sent by iPhone

1 0

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

1 0

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

3 3

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

6 9

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

3 2

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

1 0

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

3 2

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

1 0

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

29 Jan '13

Davi, This looks to me like you tried installation using e.g. the fc14 installer (that has a glibc "too new" for SL6), and installed with the fc3 on top of that (SL6 works well with the fc13 or lower installer). Since the installers write to the same directory, the fc3 installer finds that the files are already there and does basically nothing that would fix the problem, i.e. replace the binaries and libs. So just remove the /usr/local/phenix-1.8.1-1168 directory (or its contents) before you try a different installer. (Side note: maybe the installer should do that automatically, but there are probably reasons why it doesn't) HTH, Kay On 01/29/2013 12:31 AM, phenixbb-request(a)phenix-online.org wrote: > Message: 5 > Date: Fri, 25 Jan 2013 16:15:01 -0800 > From: Davi de Miranda Fonseca<davi.fonseca(a)ntnu.no> > To: phenixbb(a)phenix-online.org > Subject: [phenixbb] Unable to install phenix 1.8.1-1168 on Scientific > Linux 6.3 64 bits > Message-ID:<51032005.9040800(a)ntnu.no> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear all, > > I am unable to install phenix 1.8.1-1168 on Scientific Linux 6.3 64 > bits. Hence, I would greatly appreciate any 2 cents (or diamonds). > > 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. > This time it went through most of the installation but failed during the > configuration of phenix packages. > > **** Here is my shell output: > > [root@scientifix phenix-installer-1.8.1-1168]# ./install > > ========================================================================== > PHENIX Installation > > version: 1.8.1 > release tag: 1168 > machine type: intel-linux-2.6-x86_64 > source machine type: intel-linux-2.6-x86_64 > OS version: linux > user shell: /bin/bash > destination: /usr/local > ========================================================================= > > ========================================================================== > Installing from binary bundle > ========================================================================== > > bundle file: > bundle-1.8.1-1168-intel-linux-2.6-x86_64.tar.gz > PHENIX installation source directory set to: > /tmp/phenix-installer-1.8.1-1168 > PHENIX installation target directory<PHENIX_LOC> set to: > /usr/local/phenix-1.8.1-1168 > PHENIX installation build directory set to: > <PHENIX_LOC> /build/intel-linux-2.6-x86_64 > PHENIX temporary build directory set to: > build-binary/intel-linux-2.6-x86_64/scientifix/tmp > PHENIX installation log directory set to: > build-binary/intel-linux-2.6-x86_64/scientifix/log > > ==== warning: "/usr/local/phenix-1.8.1-1168" already exists ==== > ==== warning: cannot determine installation time-stamp, proceeding ==== > > > installing binary components > > removing existing files in > build-binary/intel-linux-2.6-x86_64/scientifix/tmp/binary > finding installed versions > finding binary versions > binary components up-to-date > the binary package will not be installed > > setting environment > > configuring PHENIX components > > Error configuring: see > /tmp/phenix-installer-1.8.1-1168/build-binary/intel-linux-2.6-x86_64/scientifix/log/binary.log > for details > > > > > ***** 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: > > ./build/intel-linux-2.6-x86_64/include/ > ./build/intel-linux-2.6-x86_64/include/phaser_defaults.params > ./build/intel-linux-2.6-x86_64/include/phaser_nma_defaults.phil > /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. > > It might be too naive from me, but would it be possible to copy > libc.so.6 from glibc-2.14 somewhere and use an option during the > installation to point to it? Any better ideas? (Like a step-wise > description used in successful installation of phenix in Scientific > Linux 6.3 64) > > Thank you for your time and help. > > Cheers, > Davi > -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

1 0

use of the file find_ncs.resolve
by Fred. Vellieux 29 Jan '13

29 Jan '13

Hi all, I do not understand how the file "find_ncs.resolve" has to be fed into the "resolve" part of Phenix. Can it be used in the GUI for an autobuild procedure? Can anyone help on this? Ta very much in advance, F. Vellieux -- F.M.D. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz 38027 Grenoble Cedex 01 France Tel: +33 438789605 Fax: +33 438785494

3 2

Add restraints between base-pairs in GUI & structures comparison
by Xiang Li 28 Jan '13

28 Jan '13

Hi everyone, I am a new user of Phenix and have a few questions asking for help. 1 I worked on a DNA structure and wanted to add restraints during the refinement. I used GUI version and chose "secondary structure restraints"->"restraint base pairs". However, there were some distortion of the base pairing after refinement. Is there a way to assign the base pairing between specific base pairs and force the base pairings in the GUI version? 2 I want to compare two DNA structures to see the RMSD. Each of them were composed of 4 strands. Seems "structure comparison" software can not work with such multiple strands DNA structures. Do you have any suggestions on how to do the comparison please? Thank you very much for your reply! Sincerely, Xiang

2 3

multiple occupancy
by Damian Niegowski 28 Jan '13

28 Jan '13

Hi all, I´m trying to refine a dataset which seems to have two different ligands with partial occupancy in the same active site. How do you refine this? When I put them over each other with say 50/50 occupancy Phenix either moves the ligands apart or mashes the two molecules into one strange composite ligand. In Refmac this works without any special settings, it accepts the occupancy distribution between the ligands. Any ideas? Regards, Damian Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegowski(a)ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39

3 2

Unable to install phenix 1.8.1-1168 on Scientific Linux 6.3 64 bits
by Davi de Miranda Fonseca 27 Jan '13

27 Jan '13

Dear all, I am unable to install phenix 1.8.1-1168 on Scientific Linux 6.3 64 bits. Hence, I would greatly appreciate any 2 cents (or diamonds). 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. This time it went through most of the installation but failed during the configuration of phenix packages. **** Here is my shell output: [root@scientifix phenix-installer-1.8.1-1168]# ./install ========================================================================== PHENIX Installation version: 1.8.1 release tag: 1168 machine type: intel-linux-2.6-x86_64 source machine type: intel-linux-2.6-x86_64 OS version: linux user shell: /bin/bash destination: /usr/local ========================================================================= ========================================================================== Installing from binary bundle ========================================================================== bundle file: bundle-1.8.1-1168-intel-linux-2.6-x86_64.tar.gz PHENIX installation source directory set to: /tmp/phenix-installer-1.8.1-1168 PHENIX installation target directory <PHENIX_LOC > set to: /usr/local/phenix-1.8.1-1168 PHENIX installation build directory set to: <PHENIX_LOC > /build/intel-linux-2.6-x86_64 PHENIX temporary build directory set to: build-binary/intel-linux-2.6-x86_64/scientifix/tmp PHENIX installation log directory set to: build-binary/intel-linux-2.6-x86_64/scientifix/log ==== warning: "/usr/local/phenix-1.8.1-1168" already exists ==== ==== warning: cannot determine installation time-stamp, proceeding ==== installing binary components removing existing files in build-binary/intel-linux-2.6-x86_64/scientifix/tmp/binary finding installed versions finding binary versions binary components up-to-date the binary package will not be installed setting environment configuring PHENIX components Error configuring: see /tmp/phenix-installer-1.8.1-1168/build-binary/intel-linux-2.6-x86_64/scientifix/log/binary.log for details ***** 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: ./build/intel-linux-2.6-x86_64/include/ ./build/intel-linux-2.6-x86_64/include/phaser_defaults.params ./build/intel-linux-2.6-x86_64/include/phaser_nma_defaults.phil /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. It might be too naive from me, but would it be possible to copy libc.so.6 from glibc-2.14 somewhere and use an option during the installation to point to it? Any better ideas? (Like a step-wise description used in successful installation of phenix in Scientific Linux 6.3 64) Thank you for your time and help. Cheers, Davi

2 1

Fwd: WCPCW 21
by Nathaniel Echols 25 Jan '13

25 Jan '13

---------- Forwarded message ---------- From: "Williams, John Charles" <jwilliams(a)coh.org> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Date: Fri, 25 Jan 2013 16:22:00 -0800 Subject: WCPCW 21 All A couple of people requested an extra day or two to register. So we have extended the standard registration fee once more to Tuesday, Jan 29th. As we have to submit our room list Feb 1 to get the room rates at discount, this has to be the last extension. Of note, the meeting is 'all inclusive' - registration includes the meeting, lodging, and all meals (breakfast, lunch and dinner, coffee breaks, and social hours). That said, WCPCW21 is quite full, but we can accommodate a few more. In addition, we have not yet started to select posters for oral presentations. So it is still possible, especially for graduate students and postdocs, to give an oral presentation. Look forward to meeting every one in Monterey! Best, John

1 0

RapiData: Seats are available - the deadline is in 10 days for our course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 25 Jan '13

25 Jan '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) =========================================================================

1 0

B-factor calculation
by Wei Shi 24 Jan '13

24 Jan '13

Hi guys, I am wondering how I can calculate average B-factor in phenix GUI. I read from an old post saying that, the following will give me complete statistics about B-factors, but in pdbtools in phenix GUI, I didn't find how to show adp statistics. phenix.pbdtools your_model.pdb --show-adp-statistics Besides, I am wondering how I can find the B-factor for each residue and plot the variation of B-factor by residue. Thank you so much! Best, Wei

3 2

phenix.refine crash due to MTZ input
by wtempel 23 Jan '13

23 Jan '13

Hello, this may perhaps fall under "garbage in, garbage out". The following reflection results in the appended stack trace. Would it be reasonable to instead just treat such reflection as missing? Best regards, Wolfram Tempel <mtz.dmp> RFREE F_r1lo1 SIGF_r1lo1 DANO_r1lo1 SIGDANO_r1lo1 F_r1lo1(+) SIGF_r1lo1(+) F_r1lo1(-) SIGF_r1lo1(-) ISYM_r1lo1 IMEAN_r1lo1 SIGIMEAN_r1lo1 I_r1lo1(+) SIGI_r1lo1(+) I_r1lo1(-) SIGI_r1lo1(-) 20 4 54 11 None None -3.61389 15.223 19.349 9.78972 22.9629 11.6577 0 -227.641 69.6184 -205.607 83.633 -277.365 125.635 </mtz.dmp> <trace> Traceback (most recent call last): File "Blah/phenix-1.8-1069/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "Blah/phenix-1.8-1069/phenix/phenix/refinement/command_line.py", line 74, in run master_params=customized_master_params) File "Blah/phenix-1.8-1069/phenix/phenix/refinement/command_line.py", line 274, in __init__ reflection_file_server = self.reflection_file_server() File "Blah/phenix-1.8-1069/phenix/phenix/refinement/command_line.py", line 793, in reflection_file_server err=self.log) File "Blah/phenix-1.8-1069/cctbx_project/iotbx/reflection_file_utils.py", line 448, in __init__ force_symmetry=self.force_symmetry)) File "Blah/phenix-1.8-1069/cctbx_project/iotbx/reflection_file_reader.py", line 209, in as_miller_arrays base_array_info=base_array_info) File "Blah/phenix-1.8-1069/cctbx_project/iotbx/mtz/__init__.py", line 502, in as_miller_arrays dataset=dataset) File "Blah/phenix-1.8-1069/cctbx_project/iotbx/mtz/__init__.py", line 610, in group_columns group = self.extract_delta_anomalous(*labels) RuntimeError: cctbx Error: Invalid combination of values while extracting anomalous array from columns: F_r1lo1, SIGF_r1lo1, DANO_r1lo1, SIGDANO_r1lo1, hkl=(20,4,54) [tip: "phenix.mtz.dump --show_column_data file_name" is available for inspecting the MTZ file] </trace>

2 1

Re: [phenixbb] Phenix for Ubuntu 12.04
by Kay Diederichs 23 Jan '13

23 Jan '13

Hi Eugene, Nat, apt-get install libjpeg62 was indeed useful. After installing that, the GUI starts but I get the error AssertionError : Traceback (most recent call last): File "/usr/local/phenix/phenix-dev-1269/build/intel-linux-2.6-x86_64/../../phenix/wxGUI2/command_line/main.py", line 22, in <module> run(sys.argv[1:]) File "/usr/local/phenix/phenix-dev-1269/build/intel-linux-2.6-x86_64/../../phenix/wxGUI2/command_line/main.py", line 17, in run wxapp = App.PhenixApp(args) File "/usr/local/phenix/phenix-dev-1269/phenix/wxGUI2/App.py", line 58, in __init__ wx.App.__init__(self, 0) File "/usr/local/phenix/phenix-dev-1269/build/intel-linux-2.6-x86_64/base/lib/python2.7/site-packages/wx-2.8-gtk2-ansi/wx/_core.py", line 7981, in __init__ self._BootstrapApp() File "/usr/local/phenix/phenix-dev-1269/build/intel-linux-2.6-x86_64/base/lib/python2.7/site-packages/wx-2.8-gtk2-ansi/wx/_core.py", line 7555, in _BootstrapApp return _core_.PyApp__BootstrapApp(*args, **kwargs) File "/usr/local/phenix/phenix-dev-1269/phenix/wxGUI2/App.py", line 101, in OnInit self.start_gui() File "/usr/local/phenix/phenix-dev-1269/phenix/wxGUI2/App.py", line 174, in start_gui self.launch_main() File "/usr/local/phenix/phenix-dev-1269/phenix/wxGUI2/App.py", line 453, in launch_main frame = PhenixGUI() File "/usr/local/phenix/phenix-dev-1269/phenix/wxGUI2/Home/Main.py", line 37, in __init__ wx.CAPTION | wx.CLIP_CHILDREN) File "/usr/local/phenix/phenix-dev-1269/phenix/wxGUI2/MainWindow.py", line 229, in __init__ PhenixFrameBase.__init__(self, parent) File "/usr/local/phenix/phenix-dev-1269/phenix/wxGUI2/MainWindow.py", line 36, in __init__ assert self.project is not None AssertionError -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz

2 1