- phenixbb - phenix-online.org

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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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".

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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

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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

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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

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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

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Fwd: WCPCW 21
by Nathaniel Echols 26 Jan '13

26 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

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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) =========================================================================

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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

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phenix.refine crash due to MTZ input
by wtempel 24 Jan '13

24 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>

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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

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Phenix for Ubuntu 12.04
by Kay Diederichs 23 Jan '13

23 Jan '13

Dear all, coming from RedHat Linux, I have a difficult time to install the latest nightly phenix build on a 64bit Ubuntu 12.04 LTS notebook. (I must confess that I did not try any older or stable releases, like 1.8.1) The reason why I did not install SL6 on the notebook is that it comes with Windows installed on fake RAID. Since I don't want to get rid of Windows completely, and thus can only take half of the disk for Linux, I wanted to use Ubuntu which offers an alternate installer supporting fake RAID. I tried the FC3 binary installer (which is offered by default), as well as the FC8 FC12 FC14 installers. Installation works, but upon startup libjpeg.so.62 is missing (libjpeg.so.80 is installed but they are incompatible). So I tried the source installer, but that fails with ERROR: installation of xrender failed ERROR: installation of xft failed ERROR: installation of cairo failed ERROR: installation of pango failed ERROR: installation of gtk failed ERROR: installation of gtk-engine failed ERROR: installation of wxgtk failed ERROR: installation of wxpython failed So I believe I should apt-get install certain packages. Does anyone know which ones? thanks, Kay -- 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".

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Problems with occupancy summation when more than two alt. conf.
by Haim Rozenberg 23 Jan '13

23 Jan '13

Hello, It seems that after "refine", the summation of occupancies is not always equal to 1.00 when more than two alternative conformations are defined in the pdb. In recently refined structures we were surprise to find 1.01 instead of 1.00 (Big deal ??? Yes, for the deposition/validation!). We didn't find any warning nor error messages in the corresponding log files. (phenix.refine: 1.8.1_1168) or newer, on Mac as well as Linux machines. Best regards, Haim ============================================ Haim Rozenberg, PhD. Department of Structural Biology Kimmelman Building Weizmann Institute of Science 76100 Rehovot, Israel Phone: +972-8-9344289 FAX:+972-8-9344136 E-Mail: haim.rozenberg(a)weizmann.ac.il ============================================ "Quis custodiet ipsos custodes?" D.I. Iuvenalis

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structure factors for PDB deposition
by wtempel 22 Jan '13

22 Jan '13

Hello all, based on ${prefix}_001_f_model.mtz from phenix.refine, I would like to prepare a cif file with structure factors. FOBS, SIGFOBS, R_FREE_FLAGS, FMODEL, PHIFMODEL, FOM are available in (+) and (-) versions, presumably representing Bijvoet pairs. My questions are: 1) are FMODEL, PHIFMODEL the most appropriate columns for calculated amplitudes and phases for the purpose of PDB deposition? 2) I understand that the PDB sf_tool does not accommodate separate (+)/(-) columns for some of the items. A job for phenix.reciprocal_space_arrays and a reflection file without anomalous differences? Alternatively, I imagine that phenix has a tailored procedure just for the preparation of PDB deposition, but I may not have used the correct web search terms to find the instructions. Thank you in anticipation, Wolfram Tempel

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fwd: WCPCW 21 - registration deadline!
by Nathaniel Echols 21 Jan '13

21 Jan '13

---------- Forwarded message ---------- From: "Williams, John Charles" <jwilliams(a)coh.org> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Cc: Date: Mon, 21 Jan 2013 11:16:14 -0800 Subject: WCPCW 21 - registration deadline! Dear All, Today is technically the last day of standard registration rates. I have had a couple of emails this morning asking for extra time (approval by business manager, etc.). To accommodate everyone, we will extend the rate standard rates until Wednesday, Jan 23rd. Also, please submit your abstract soon. We have a significant number of people already registered and will have have to select abstracts for oral presentations. Best, John

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Structure minimization for model with rigid body
by danashah＠post.tau.ac.il 18 Jan '13

18 Jan '13

Hi all, We're interesting in performing a structure minimization for a model, while treating a part of the model as a rigid body. Is there an option for that on PDB tools via geometry minimization? Or is there another way to do that? Thank you, Dana. __ Dana Sachyani Joel Hirsch's Lab Faculty of Life Sciences Tel Aviv University Ramat Aviv, Israel e-mail: danashah(a)post.tau.ac.il

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Bug squash request
by Antony Oliver 17 Jan '13

17 Jan '13

Dear Phenix-developers, I've noticed a slightly annoying "feature" when using a reference model to help in refinement of low-resolution structures. phenix.refine seems to take it's crystal parameters and space-group from whichever PDB was loaded last, even after setting one PDB as the "reference model" and the other as the "Input model". When running phenix.refine it gives you a nice error message telling you that the space group information is incorrect, and that you may have used the reference model's parameters by mistake… But surely, it should just (by default) only take (check?) the cell parameters and space group information from the "Input PDB"? With thanks, Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oliver(a)sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512

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Still can't get refinement of anomalous groups to work
by Brennan Bonnet 16 Jan '13

16 Jan '13

Hi all, I'm still working on this pesky anomalous group refinement problem. Originally, the problem was that the output from AutoBuild no longer retained the anomalous data. To fix this, I used the Phenix reflection file editor and combined exptl_fobs_phases_freeR_flags.mtz (which is automatically entered as input when running phenix.refine from AutoBuild) with the F+ F- values from my original reflection data. Now when I try to run refinement I get this error message: "This model appears to have previously been refined against a different set of R-free flags. Please resolve the mismatch." I find this strange since I am only modifying the file that phenix.refine tries to use anyway. How do I fix this problem? Thanks, ~Brennan~

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18 Days to the deadline: Please apply for RapiData 2013, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 16 Jan '13

16 Jan '13

We are offering 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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how to modify C-D bond length restraints in phenix?
by Maxime Cuypers 16 Jan '13

16 Jan '13

Hi, i am refining a perdeuterated neutron structure and have noticed a lot of positive density aside the D atoms on aliphatic and aromatic side chains. just in the alignment of C-D bonds (C-D then +), suggesting that phenix.refine constraints these bond lengths too short in my case. i tried automatic weights for geometry refinement and unrestrained specific C-D refinement but it is not satisfactory. then i found the following funny distances (angströms) in the pdb database neutron structures: 3KYX: program: Phenix.refine D-prot Distances: C-D aromatics = 0.93-0.94 C-D aliph. = 0.98 1CQ2 Program : xplor3.1 D-protein (despite the atoms being labelled as H according to abstract) Distances: C-D aromatics = 1.06-1.08 C-D aliph. = 1.08 4FC1 H-protein Distances: program: Phenix.refine C-H aromatics = 0.93 C-H aliph. = 0.97 1VCX H-protein program: CNS Distances: C-H aromatics = 1.06-1.10 C-H aliph. = 1.09 those neutron C-D/C-H bond lengths in pdb seem pretty much inconsistentto me. So it seems that phenix.refine uses C-D/ C-H bonds restrains that are different to other programs to below 1.0 Ang. ( ca. 0.10 A differences) how can i change the restraints to make it all longer bond lengths for C-D only? with a .cif file? i saw that phenix uses the CCP4 monomer library but the one in : /usr/local/phenix-.../chem_data/mon_lib/list only seem to be applying modifications. any clue on how to specifically modify the restraints parameters on C-D bonds would be very appreciated. Thanks, Maxime

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Macromolecular Crystallography School announcement : 2013 in Uruguay
by Alejandro Buschiazzo 16 Jan '13

16 Jan '13

Dear Colleagues, We are pleased to announce the *second Macromolecular Crystallography School 2013 *at the Institut Pasteur de Montevideo (Uruguay). All details can be found at www.pasteur.edu.uy/mx2013 <http://www.pasteur.edu.uy/mx2013> *Title:* "Macromolecular Crystallography School 2013: From data processing to structure refinement and beyond" *Dates:*April 9th-17th, 2013. *Site:*Institut Pasteur de Montevideo (Montevideo), Uruguay *The workshop content:* Conceived to provide theoretical background and hands-on abilities in the use of computational tools to exploit X ray diffraction data. Through lectures, tutorials and hands-on trouble-shooting, the students will be trained in state-of-the-art macromolecular crystallography. Particular emphasis will be given to data processing, phasing/structure determination and model refinement/validation. The workshop will feature authors and experts of many modern crystallographic software packages. This workshop represents the continuation within the series started in 2010 (http://www.pasteur.edu.uy/mxcourse) on Macromolecular Crystallography. In this opportunity it is being co-organized by the Center for Structural Biology of the Mercosur CeBEM (www.cebem.org.ar <http://www.cebem.org.ar>), jointly with the Collaborative Computational Project Number 4 (CCP4 -- UK www.ccp4.ac.uk <http://www.ccp4.ac.uk>). Support from the Institut Pasteur International Network, the International Union of Crystallography and Institut Pasteur de Montevideo is also greatly acknowledged. *Applicants:* Graduate students, postdoctoral researchers and young scientists are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets so they can be used during the workshop's hands-on sessions. There is no registration fee. Support for accommodation, per diem and local transportation will be provided to all participants from abroad. Support to cover travel expenses will be considered on a case-by-case basis. Specific requests should be well-grounded as we will only be able to select a limited number. *Application:* Application *deadline is February 10, 2013*. Application form, the program, contact info and other details can be found at www.pasteur.edu.uy/mx2013 <http://www.pasteur.edu.uy/mx2013> Please address further inquiries to mx2013(a)pasteur.edu.uy <mailto:[email protected]> Ronan Keegan and Alejandro Buschiazzo -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

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Heavy atoms outside of molecule
by Brennan Bonnet 15 Jan '13

15 Jan '13

Hi all, Is there an option in Phenix that will fix the heavy atom positions so that they are at their equivalent positions within the molecule? Thanks Brennan

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P3 pseudotranslation
by Ethayathulla A.S 15 Jan '13

15 Jan '13

Hello I am trying to solve a structure with P3 Pseudotranslation at 3.5A. The 3.5 dataset have cell of 150,150,200 and 5A dataset have smaller cell 150,150, 100. The data can be scaled in P321, p3221,p3121 with similar rsym (6 (54). Pointless gave me Spacegroups as P3221 or P3121 as soln. I tried Phenix.xtriage it showed me 40% Pseudotranslation peak ( 0,0,0.5) for 3.5A dataset as the c-axis is double that of 5A data. According to cell content analysis it can be dimer in 3.5A and monomer for 5A dataset. So I tried MR with both datasets with homology model build using similar fold protein. I got solns for dimer with LLGs with 1000's in P3221,P3121,P321 with 3.5A dataset. There were 28 solutions ++++++++++++++++++++++++++++++++++++++++++++++++++ SOLU SET RFZ=2.0 TFZ=8.2 PAK=0 LLG=259 TFZ==11.3 LLG=1181 TFZ==28.4 ( SOLU SPAC P 32 2 1) SOLU 6DIM ENSE partial EULER 94.4 2.7 25.5 FRAC -0.07 -1.07 -0.81 BFAC -1.00 Solution #2 annotation (history): SOLU SET RFZ=2.0 TFZ=8.2 PAK=0 LLG=225 LLG=1066 ( SOLU SPAC P 31 2 1) +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ So I refined the solns. of P3221, p321 it refined to 44/54 after that it doesn’t go down. The 0.5 Pseudotranslated molecule can been as symmetry molecule along c-axis. The packing looks very good. I have attached the image of it with native patt map. I deleted one monomer and refined to check the solution I could see clearly see the other molecule. I could see 2n+1 odd reflections to be weak. To check whether two fold can be due to twinning due to pseudotranslation I could not observe it. So I tried to see check whether the it can be P32 merohedral twinning with pseudotranslation with twinning of 0.36 (h,-h-k,-l) from yeates server. I try to use the dimer of P3212 and try for alternative spacegroup which yield me unique soln in P32. I refined the molecule four molecule which yielded me 46/49 and when I apply twinning fraction the r-factor decreases to 40/45. Similarly for 4.5A dataset I used dimer of 3.4 dataset dimer which yield me solution in P32 but cannot refine it gets struck for 45/50.I tried to use the dimer with 5A dataset I get unique solu and refine with merohedral twinning the r/freeR goes to 38/57. How I can check whether it is P32 merohedral twinning with Pseudotranslated or P3221. Also the patterson analysis another peak of height 4% ( 0.050, 0.102, 0.495 ) : 4.452 . Is it significant ? Any suggestion will be helpful Thank you Abdul ++++++++++++++++++++++++++++++++++++++++++++++++++ Patterson analyses from phenix.xtriage Frac. coord. : 0.000 0.000 0.500 Distance to origin : 103.157 Height (origin=100) : 40.427 p_value(height) : 2.740e-04 The full list of Patterson peaks is: x y z height p-value(height) ( 0.000, 0.000, 0.500 ) : 40.427 (2.740e-04) ( 0.050, 0.102, 0.495 ) : 4.452 (9.782e-01) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -- *********************************************** Dr. A.S. Ethayathulla Dept of biophysics AIIMS, new delhi ***********************************************

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fwd: Annual CCP4 summer school in USA, at APS, June 18-26
by Nathaniel Echols 14 Jan '13

14 Jan '13

---------- Forwarded message ---------- From: "Ruslan Sanishvili (Nukri)" <nukri(a)aps.anl.gov> To: phenixbb(a)phenix-online.org Cc: Date: Mon, 14 Jan 2013 17:46:48 -0600 (CST) Subject: Annual CCP4 summer school in USA, at APS, June 18-26 Dear Colleagues, We are pleased to announce the sixth annual CCP4 summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2013/index.php Title: "CCP4 school: From data collection to structure refinement and beyond" Dates: June 18 to 26. Site: Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA The school content: Data collection workshop the first two days: beamline training and data collection on GM/CA-CAT beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three Sections – lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection workshop and/or hands-on sessions. Application: Application deadline is April 5. The application form, the program, contact info and other details can be found at http: http://www.ccp4.ac.uk/schools/APS-2013/index.php Fees: There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers will arrange economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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