January 2013 - phenixbb - phenix-online.org

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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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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