- phenixbb - phenix-online.org

FW: phenixbb Digest, Vol 87, Issue 3
by Phoebe A. Rice 10 Feb '13

10 Feb '13

Hi, Although its theoretically possible, I've never had 5-Br-dU cause a problem. My approach would be to pick the strand with more T's and get every T replaced with 5-Br-dU, unless the 3' nt is a T (you pay a lot more for 3' modifications). We have had issues where crystals wouldn't grow with a heavily 5-I-dU modified DNA, presumably because Iodine is significantly bigger than a the 5-methyl of T, and it annoys the protein. If you've got good footprinting data, you may be able to guess where the protein will "care" about the surface of the major groove, and avoid putting iodines in those regions. If not, its probably faster to just order several oligos and try them all. If you've got a lot of T's and are worried about locating all those heavy atoms, I'd go for one derivative with a couple of paired 5-I-dU's (in spots where you have two T's in a row) in hopes that that will give you a toehold on solving the Patterson, and then a 2nd where every T on one strand is brominated, which may provide more phasing power. Note that both of these pop off in the x-ray beam, so collect your anomalous data first and fast. Also note that if you're lucky, you can get an extra large delta f' by subtracting the last data set from the first ("radiation induced phasing"). Hope that helps! Phoebe ++++++++++++++++++++++++++++++++++++++++++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago 773 834 1723; PRice(a)uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp

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CeBEM-CCP4 Macromolecular Crystallography Workshop 2013 at Montevideo: Application deadline extended
by Alejandro Buschiazzo 09 Feb '13

09 Feb '13

Dear Colleagues, Due to the application deadline originally scheduled for February 10, overlapping with Summer holiday dates in several South American countries, we have decided to extend the course application deadline UNTIL FEBRUARY 17, 2013. We invite all of you interested in this workshop, especially the ones that have contacted us, to take advantage of this opportunity and send your application forms (plus CV and letter of your supervisor): last days for applications open!! Find all details about the workshop and application form in www.pasteur.edu.uy/mx2013 <http://www.pasteur.edu.uy/mx2013>- for further inquiries and applications contact mx2013(a)pasteur.edu.uy <mailto:[email protected]>! *Second Macromolecular Crystallography School 2013 *at the Institut Pasteur de Montevideo (Uruguay). *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 has now been extended until February 17, 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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phaser for long thin molecule
by Ursula Schulze-Gahmen 08 Feb '13

08 Feb '13

I am doing molecular replacment for a very elongated molecule in phaser. I would like to try different values for the maximum patterson cutoff but I am not sure which parameter I need to change in the phenix version of phaser. Does somebody have experience with this? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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How to model domain-wide disorder in Phenix.refine (turn off bump interactions) ?
by Phil Jeffrey 08 Feb '13

08 Feb '13

Hi, I've got a pernicious problem where the electron density for one domain appears to extensively interpenetrate another similar domain. I'm in the process of trying to work out things like: MR solution in the wrong space group courtesy of pseudo-centering. In the meanwhile I want to model it as interpenetrating domains, and need to turn off VdeW bumps at the domain (chain) level of structure. I can't just model it as a infinite list of alternate locations. I (think) I remember how to do this in CNS (constraints interaction), but is there a way to do this in phenix ? I could not track down a particularly promising section of either the manual or the .def/eff file(s). Thanks Phil Jeffrey Princeton

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Designing heavy atom positions on my DNA crystal
by Xiang Li 07 Feb '13

07 Feb '13

Hi everyone, I am trying to grow my DNA crystal with bromide derivatives. The content in one asymmetric unit is a 30 bp DNA duplex. I am considering about how many bromides modified bases should I use to ensurethe strong enough heavy atom signal. Also where to put these bromides? To my understanding, maybe I should put the heavy atoms at the most rigid places, avoiding the clashes and not too close to other heavy atoms. I have few experience on this and hope you could give me some help on the design. Thanks a lot! Sincerely, Xiang

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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

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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

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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

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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 >

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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>

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

01 Feb '13

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

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

01 Feb '13

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

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dzp
by Fumiaki Yumoto 31 Jan '13

31 Jan '13

Sent by iPhone

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

31 Jan '13

Folks The latest edition of the Computational Crystallography Newsletter is available at http://phenix-online.org/newsletter The table of contents is listed below. Articles cctbx tools for transparent parallel job execution in Python. I. Foundations cctbx tools for transparent parallel job execution in Python. II. Convenience functions for the impatient. Short communications Phenix / MolProbity Hydrogen Parameter Update PSI SBKB Technology Portal: A Web Resource for Structural Biologists Fitting tips #5 - What’s with water FAQ - I'm seeing a lot of CIF files. Are they all restraints? Cheers Nigel -- Nigel W. Moriarty, PhD Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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

31 Jan '13

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

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

30 Jan '13

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

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

30 Jan '13

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

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

30 Jan '13

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

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

29 Jan '13

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

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

29 Jan '13

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

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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 29 Jan '13

29 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 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

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 25 Jan '13

25 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 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>

2 1

Re: [phenixbb] Phenix for Ubuntu 12.04
by Kay Diederichs 24 Jan '13

24 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

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".

2 1

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

2 1

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

4 3

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

1 0

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

3 2

Bug squash request
by Antony Oliver 18 Jan '13

18 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

2 1

Still can't get refinement of anomalous groups to work
by Brennan Bonnet 17 Jan '13

17 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~

2 5

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

1 0

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 15 Jan '13

15 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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Ligand building/refinement woes
by Machius, Mischa Christian 14 Jan '13

14 Jan '13

I seem to be having the hardest time building/refining NADPH (PDB code NAP). When fetching this common ligand from within coot, Phenix (1.81-1168) subsequently does not seem to accept it and bombs noting all kinds of violations. When I have Phenix automatically build NAP into the density, it does place NAP (albeit completely out of otherwise quite nice density). When I then take the coordinates, read them into coot together with the CIF that Phenix writes into the ligand_build directory, placing and refinement in coot works well, but subsequent refinement in Phenix, using the very same CIF, again bombs. Since hydrogens are often an issue when going from coot to Phenix I remove them before running Refine. I have also tried just refining the coordinates as they came out of ligand_build. But Phenix still bombs and doesn't seem to accept its own CIF. I would have thought that a ligand as common as NAP wouldn't require a lot of gymnastics, perhaps not even reading CIF information, and that it would go all automatically.That's probably too optimistic on my part. It's probably something silly, but I can't figure out what it is. Any ideas? Many thanks in advance, MM

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Fwd: WCPCW21
by Nathaniel Echols 14 Jan '13

14 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, 14 Jan 2013 10:29:12 -0800 Subject: WCPCW21 Dear All, The West Coast Protein Crystallography Workshop is rapidly approaching. The standard rates close Jan 21st. Also, we are now able to accept credit cards. Due to IT security issues, the CC number needs to be called in to Ariadna Bello, senior secretary in Dept of Molecular Medicine, City of Hope. Finally, please submit your abstracts as soon as possible as we will start to select oral presentations. Best, John

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Electron Density
by CPMAS Chen 14 Jan '13

14 Jan '13

Thanks, Nat, If the density level(map or coefficient) of phenix is not an absolute level, then I really do not need to worry what shows up by coot. I used the Fourier map generated by phenix, .mtz file. Thanks! 6. density level (CPMAS Chen) > 7. Re: density level (Nathaniel Echols) > 9. Re: density level (Pavel Afonine) > > > > ------------------------------ > > > Message: 7 > Date: Sun, 13 Jan 2013 12:21:00 -0800 > From: Nathaniel Echols <nechols(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] density level > Message-ID: > <CALeAa1Mty9= > U-CFcmhJ1ZRWAiuXMeOS0RHVT4YtXpOVBO0EDyQ(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Sun, Jan 13, 2013 at 11:38 AM, CPMAS Chen <cpmasmit(a)gmail.com> wrote: > > I recently updated my old phenix-1.6.4-486 to phenix-dev-1266. To my > > surprise, the absolute electron density on the 2Fo-Fc map is quite > > different. > > The electron density maps (or coefficients) generated by Phenix are > not on an absolute scale, and the values displayed by Coot are more or > less irrelevant. The scaling method changed significantly between > 1.6.4 and 1.8, so I'm not surprised that the map levels did too. > > > By the way, is there a simple way to keep only F and SIGF column of the > > autoxds generated truncate.mtz via phenix? the GUI does not allow to > reduce > > columns. I normally use IMEAN and SIGIMEAN to do refinement, but this may > > not be necessary as it is pointed in the maillist, since the intensity is > > already transformed to amplitude after truncation in autoxds. > > > > I can specify labels by xray_data.labels = "F, SIGF", but apparently > phenix > > treats it as containing anomalous data. the following is extracted from > the > > refine pdb file > > > > MIN(FOBS/SIGMA_FOBS) : 1.16 > > REMARK 3 COMPLETENESS FOR RANGE (%) : 97.11 > > REMARK 3 NUMBER OF REFLECTIONS : 143207 > > REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 73247 > > > > Also, in the auto generated def file, > > xray_data.labels = "F, SIGF, DANO, SIGDANO" > > This is intentional - why would you want to throw out information? > However, you can always use either the reflection file editor (in the > latest builds) or the French & Wilson GUI to convert IMEAN to F. > > > -Nat > > > > > ------------------------------ > > Message: 9 > Date: Sun, 13 Jan 2013 21:19:17 -0800 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] density level > Message-ID: <50F39555.8000000(a)lbl.gov> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hi, > > what kind of file you use to see the map in Coot: Fourier map > coefficients (MTZ file) or actual map (CCP4 binary formatted file with > the map)? I need to know this before offering a first guess on what may > be the reason for this. > > Pavel > > On 1/13/13 11:38 AM, CPMAS Chen wrote: > > Dear PhenixBBer, > > > > I recently updated my old phenix-1.6.4-486 to phenix-dev-1266. To > > my surprise, the absolute electron density on the 2Fo-Fc map is quite > > different. > > > > https://www.dropbox.com/s/prs0z8ayb73kg9k/Screenshot_sigma.png > > > > At the same sigma level(1.5), the absolute density of the violet map > > is 0.32e/A^3 (phenix-dev-1266), while that of the blue map is > > 0.01e/A^3(phenix-1.6.4-486). Besides the different phenix used, there > > is no other difference on the data and model used. > > > > Sam encountered a similar problem on the density. > > > > http://phenix-online.org/pipermail/phenixbb/2012-December/019226.html > > > > By the way, is there a simple way to keep only F and SIGF column of > > the autoxds generated truncate.mtz via phenix? the GUI does not allow > > to reduce columns. I normally use IMEAN and SIGIMEAN to do refinement, > > but this may not be necessary as it is pointed in the maillist, since > > the intensity is already transformed to amplitude after truncation in > > autoxds. > > > > I can specify labels by xray_data.labels = "F, SIGF", but apparently > > phenix treats it as containing anomalous data. the following is > > extracted from the refine pdb file > > > > MIN(FOBS/SIGMA_FOBS) : 1.16 > > REMARK 3 COMPLETENESS FOR RANGE (%) : 97.11 > > REMARK 3 NUMBER OF REFLECTIONS : 143207 > > REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 73247 > > > > Also, in the auto generated def file, > > xray_data.labels = "F, SIGF, DANO, SIGDANO" > > > > Or there is a work round for this issue? > > > > Thanks! > > > > -- > > > > *************************************************** > > > > Charles Chen > > > > Research Associate > > > > University of Pittsburgh School of Medicine > > > > Department of Anesthesiology > > > > ****************************************************** > > > > > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > >

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density level
by CPMAS Chen 14 Jan '13

14 Jan '13

Dear PhenixBBer, I recently updated my old phenix-1.6.4-486 to phenix-dev-1266. To my surprise, the absolute electron density on the 2Fo-Fc map is quite different. https://www.dropbox.com/s/prs0z8ayb73kg9k/Screenshot_sigma.png At the same sigma level(1.5), the absolute density of the violet map is 0.32e/A^3 (phenix-dev-1266), while that of the blue map is 0.01e/A^3(phenix-1.6.4-486). Besides the different phenix used, there is no other difference on the data and model used. Sam encountered a similar problem on the density. http://phenix-online.org/pipermail/phenixbb/2012-December/019226.html By the way, is there a simple way to keep only F and SIGF column of the autoxds generated truncate.mtz via phenix? the GUI does not allow to reduce columns. I normally use IMEAN and SIGIMEAN to do refinement, but this may not be necessary as it is pointed in the maillist, since the intensity is already transformed to amplitude after truncation in autoxds. I can specify labels by xray_data.labels = "F, SIGF", but apparently phenix treats it as containing anomalous data. the following is extracted from the refine pdb file MIN(FOBS/SIGMA_FOBS) : 1.16 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.11 REMARK 3 NUMBER OF REFLECTIONS : 143207 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 73247 Also, in the auto generated def file, xray_data.labels = "F, SIGF, DANO, SIGDANO" Or there is a work round for this issue? Thanks! -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Refining anomalous groups
by Brennan Bonnet 13 Jan '13

13 Jan '13

Hi All, I hope everyone had relaxing holidays to begin the new year. I am back to work trying to refine anomalous groups using phenix.refine. I have managed to merge my files so that my exptl_fobs_phases_flags_1_with_hl_anom.mtz now contains F(+), SIGF(+), F(-), SIGF(-). Now I have a new problem which was not occurring before the break. Usually I check the box for "Anomalous groups", then select "Modify selections for: Anomalous groups" which brings up a screen for atom selection and definition of f' and f''. In the past, clicking on the View/pick button launches Coot for selection of the atoms. Sadly, now clicking on the View/pick doesn't launch Coot and instead crashes Phenix. Does anyone else have this problem or know how to fix it? Please help! Thanks, ~Brennan~

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Problem rebuilding ligand structure
by bsubedi＠btk.fi 12 Jan '13

12 Jan '13

Hi, I am using Phenix 1.0-1069 for refinement and coot 0.7-pre-1 for visualization and rebuilding. I used SMILES in coot to build the ligand and then merged them with PDB.I had to do this as a separate step for both chains and the .cif file so produced was not accepted for refinement. I used readyset to obtain the restrains for refinement using .pdb file, even though my refinement works, when i try to run real build refine in coot I get this error message: Failed to match (to the dictionary) the following model atom names: HB3 O6 C10 C11 C12 O7 C13 O5 C8 C9 ...... That would cause exploding atoms, so the refinement didn't start. Could someone help me with fixing this problem. Best regards, Bishwa

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symmetry related bond restraint in R3 space group
by Xiang Li 11 Jan '13

11 Jan '13

I am trying to add some restraints between symmetric molecule with symmetry operation. However, I found it is not correct to use the operation information directly provided in Coot. The crystal I worked on has R3 symmetry. The symmetry operation in Coot shows to be -x+y,-x,z+ (1,1,0) and it did not work in Phenix refine. I read one previous email on this topic about the difference of symmetry operation in Coot and Phenix. However, I do not know how to do the conversion between the two when the numbers changed. Could you help me to work out on correct the symmetry operation in Phenix and talk some more on how to do the conversion please? I really appreciate your help! Sincerely, Xiang

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