- phenixbb - phenix-online.org

Re: [phenixbb] On Mac two separate installations?
by Joseph Noel 27 Jul '13

27 Jul '13

Thanks Nat! I am trying out the new "Featured Enhanced Map" option. Preliminary analysis says it really helps! Also, following the protocol as outlined by Andy Karplus in his Science paper on data processing using data extending to CC1/2's near 0.2. Both together seem to really extend the resolution of my datasets and also improve refinement! ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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Fwd: Course on “Structure and Function of Membrane Proteins- a multidisciplinary approach”
by Nathaniel Echols 26 Jul '13

26 Jul '13

---------- Forwarded message ---------- From: Jose Artur Brito <jbrito(a)itqb.unl.pt> To: phenixbb(a)phenix-online.org Date: Fri, 26 Jul 2013 15:58:01 +0100 Subject: Course on “Structure and Function of Membrane Proteins- a multidisciplinary approach” Dear colleagues, We would like to announce the Instruct-sponsored 4-day course “Structure and Function of Membrane Proteins- a multidisciplinary approach”, to be held at ITQB, Oeiras (nearby Lisbon), Portugal, from 5 to 8 November 2013. The course will address several techniques for the structural and functional characterization of membrane proteins, with special emphasis on Macromolecular Crystallography, Mass Spectrometry, Electron Microscopy and Nuclear Magnetic Ressonance. The information provided by each technique, their applications in biological systems, major benefits and limitations will be discussed. The course is organized with lectures in the mornings and interactive tutorials in the afternoons. In addition, the selected applicants are grouped and each group works on a case study (based on 2-3 papers covering techniques of interest and a questionnaire) and gives a presentation at the end of the course. The course is aimed primarily at PhD students, young Post-Doctoral researchers and others with research activities involving structural biology of membrane proteins. Participants will be limited to 20. Candidate selection will be based on a short CV, a motivation letter from the applicant, and a recommendation letter from the supervisor. Registration deadline is September 16, please send your application to membstruct2013(a)itqb.unl.pt . More information can be found at http://www.itqb.unl.pt/membstruct2013 The organizing commission, Margarida Archer (ITQB-UNL), Carlos Cordeiro (FC-UL) and José A. Brito (ITQB-UNL) -- ************************************************ * José Artur Brito, PhD * * * * Post-Doctoral Fellow * * Membrane Protein Crystallography Lab * * Instituto de Tecnologia Química e Biológica * * Oeiras - Portugal * * * * Tel.: +351.21.446.97.61 * * Fax: +351.21.443.36.44 * * * * E-mail: jbrito(a)itqb.unl.pt * * URL: http://mx.itqb.unl.pt * ************************************************

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Linux distribution question: who needs the FC3 build?
by Nathaniel Echols 25 Jul '13

25 Jul '13

Dear users, We are in the process of rearranging our server room and changing the way we do the nightly builds. One step of this will be retiring the bulky and ancient boxes which run Fedora 3, and standardizing on slightly more modern OSes. (Including Ubuntu-specific builds, as well as the usual Fedora/RedHat/CentOS base.) I know that some people have found that the Fedora 8 x86_64 build does *not* run properly on their systems, but the Fedora 3 build does. Could anyone who has firsthand experience with this please contact me off-list and tell me exactly which distribution and version you are running? We can't cover all possible combinations (sorry Gentoo users), but I'd like to get some idea what is still problematic. thanks, Nat

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Refinement using a homolog as a reference
by Joshi, Amar (Dr.) 25 Jul '13

25 Jul '13

Hi, I am refining ligand-protein complexes at 3.2Å dataset with a human protein. My Rfree is ~0.34 but my ramachandran stats are concerning me: 85% favoured, 4.5% disallowed. The structure of a yeast homolog has been deposited at 2.4Å resolution. The yeast structure contains additional loops but is ~55% identical to the human protein. The overall conformation between the homologs is very similar. Can I use this as a reference model? Should I prune the reference model? Will different numbering schemes affect the refinement? Many thanks, Amar

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Re: [phenixbb] Linux distribution question: who needs the FC3 build?
by Nathaniel Echols 25 Jul '13

25 Jul '13

On Wed, Jul 24, 2013 at 2:56 PM, Edward A. Berry <BerryE(a)upstate.edu> wrote: > Would that be the end of support for 32-bit linux? Or would you build > i686 version on a later version? (Or is it possible to run 64 bit > executable on 32- bit operating systems with some kind of compatibility > libraries and 64-bit capable hardware?) > > I have one Fc8 32 bit machine which I don't want to upgrade, but I don't > really need to run phenix on it. Just to clarify: we will continue distributing 32-bit Linux indefinitely (although probably on fewer platforms than 64-bit), and we will at least support Fedora 8 at a minimum for a while, since our most important development system is still running it. The question is really related to how ancient a distribution we need to support, and what scenarios are especially difficult for binary cross-compatibility. -Nat

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calculate map from ensemble refinement
by Bard, Joel 24 Jul '13

24 Jul '13

Hi- I ran phenix.ensemble refinement which worked very nicely but crashed during map output. I think this was my fault for using a parameter file that had map_type = None (I didn't look and assumed the default was reasonable). I would like to calculate maps after the fact. Is there a way to run the map calculation on the output ensemble pdb file and reflection data? I tried phenix.maps which choked on the huge ensemble. Thanks, Joel

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Group ADP refinement
by joseph Lyons 24 Jul '13

24 Jul '13

Dear phenixbb. I am currently running phenix 1.8.2-1309. My goal is to use group ADP with 2 b-factors per residue for the protein and individual b-factors for solvent. However, this does not seem to be working even though the system seems to recognise what I want to do. The refinement output gives what looks like individual b-factor refinement... ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4048 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 127 aniso = 0) group_adp = True (3921 atoms in 967 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 atoms) group_anomalous = False In troubleshooting it appears that with Group ADP with 2 b-factors per residue, the solvent B-factors are not being refined, i.e., remaining at the Wilson B that I set previously. For Group ADP with 1 b-factors per residue - everything appears to refine OK. Any help would be greatly appreciated, Regards, Joe

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Re: [phenixbb] How do I turn off sidechain rotamer fitting? (Pavel Afonine)
by Joseph Noel 24 Jul '13

24 Jul '13

Dear Pavel, To clarify, in the latest nightly build, 1435, do you have to click on real space refinement to carry out side chain rotamer fitting? If you just refine xyz I assume side chain rotamer fitting is not enabled, correct? Joe Noel ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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Re: [phenixbb] Phenix "hangs" on a Mac?
by Joseph Noel 24 Jul '13

24 Jul '13

Hi Nat, Will replicate and send you the information. Its unrelated to Ramachandran restraints as it occurs intermittantly when doing just regular tasks. I can always tell early as it never seems to get past the first steps of the refinement protocol - in essence - it never starts xyz refinement. Just sits there. I abort and restart and it then goes fine. I'm running Mac OSX 10.8.4 Joe ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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Post-doc position for SAXS at the MAX IV Laboratory
by Marjolein Thunnissen 23 Jul '13

23 Jul '13

The MAX IV laboratory in Lund has opened a position for a Postdoctoral fellow to strengthen the biological SAXS environment at the current SAXS beam line. The position will be for two years and is embedded in the BIOSTRUCT-X EU program. Full information of the position is available at: http://admin.lu.se/o.o.i.s?id=22598&Dnr=554436&Type=E as well as who to contact for more information. Information about the MAX IV laboratory can be obtained at www.maxlab.lu.se<http://www.maxlab.lu.se> . best regards Marjolein Thunnissen ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)76-632 0417 Associate Professor Fax +46-(0)46-22 24692 Dept of Biochemistry and Structural Biology, Lund University http://www.mps.lu.se<http://www.mps.lu.se/> PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator MX (The MAX IV Laboratory): I911 and BioMAX ________________________________________________________________________

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Phenix "hangs" on a Mac?
by Joseph Noel 23 Jul '13

23 Jul '13

Has anyone had a problem when using Phenix refine through the GUI on a Mac wherein the program after hitting Run locally starts but then hangs without proceeding? Seems to happen to me about one out of five times I run refine and always hangs when I experiment with ramachandran restraints for only a portion of the polypeptide chain. I've tried letting things alone for several hours and nothing happens. I can abort and then often resubmit and it then runs fine (except for rama restraints). I've found this happens with both nightly builds and stable releases. I am currently running the latest nightly build 1439. ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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On Mac two separate installations?
by Joseph Noel 23 Jul '13

23 Jul '13

Does one have to install both the GUI and command line installers on a Mac if one wants to have the option of running using the command line (for command line only options in nightly builds) and the GUI? ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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mr_rosetta pause & resume
by Karolina Michalska 23 Jul '13

23 Jul '13

Hello everybody, Is there a way to pause an mr_rosetta run and resume it with a different number of processors? Thanks, Karolina

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Registration open: "The Future of Microfocus Protein Crystallography"
by Marjolein Thunnissen 22 Jul '13

22 Jul '13

Dear all, I would like to remind you on a workshop on "The Future of Microfocus Protein Crystallography" which will take place at the MAX IV User meeting on the 24th and the 25th of September, 2013, in Lund, Sweden. Recent developments within protein crystallography methods in combination with the possibilities offered by the new upcoming synchrotron sources such as the MAX IV 3 GeV storage ring make possible exciting new ways of carrying out research within structural biology. Small microfocus beamlines with a very high flux and increased coherence will make new types of experimentation possible. The scientific possibilities will be highlighted through a series of talks by experts showing the impact of the new type of X-ray sources and microfocus beamlines on research within structural biology. The new generation of microfocus beamlines will also set a high demand on instrumentation and suitable software. For example, data collection will potentially be very fast (in milliseconds) and radiation damage will allow only a limited amount of data to be collected from each sample. New technical solutions for sample handling and presentation, data processing methods and more will be needed for these types of experiments, and these will also be presented and discussed at the workshop. Confirmed speakers include David Stuart, Daniel Wacker, Simone Weynand, Jens Preben Morth, Tove Sjögren, Richard Neutze, Janet Smith, Alke Meentz, Alexei Soares, Thomas White, Luca Jovine and Clemens Schulze-Briese The workshop is part of a process to obtain an updated proposal for the possible Phase 2b beam line MicroMAX at the upcoming new 3 GeV storage ring of MAX IV in Lund. This workshop should give the user community an opportunity to explore the scientific possibilities of a new generation of microfocus beam lines, but also it will give them the chance to contribute with specific input on their own experimental demands on the beam line. The workshop is part of the MAX IV laboratory user meeting, but there is no requirement to be a user of the facility and all that are interested are welcome . Registration is through the user meeting website: https://indico.maxlab.lu.se/indico/conferenceDisplay.py?confId=0 . The registration fees are 2000 SEK for academics and 700 SEK for junior scientists. Registration fees include all lunches and the conference dinner. Further information on this workshop can be found at https://www.maxlab.lu.se/node/1609 and for the MAX IV user meeting at https://www.maxlab.lu.se/um13 . For the organisers, Richard Neutze, Gunter Schneider and Gregers Rom Andersen Marjolein Thunnissen ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)76-632 0417 Associate Professor Fax +46-(0)46-22 24692 Dept of Biochemistry and Structural Biology, Lund University http://www.mps.lu.se<http://www.mps.lu.se/> PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator MX (The MAX IV Laboratory): I911 and BioMAX ________________________________________________________________________

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Fo-Fo map
by Xiang Li 22 Jul '13

22 Jul '13

Hi everyone, I am working on two datasets of the similar crystal design. In one of the datasets, there is an extra guest protein (might be considered as a ligand) docked in one unit cell. The two crystals have very similar unit cell size and same symmetry. I want to calculate the Fo-Fo map to see whether I could figure out where the protein is. But I got error says the symmetry of the two datasets are not the same. I have never used the "isomorphous difference map" in GUI before. Can anyone help me to figure out where I did wrong please? I have attached the mtz file that I want to compare. Btw, if the protein is not very rigidly linked with the crystal framework (~2 free residues linkage), am I supposed to see the density of the protein? Or are there any better ways for me to identify the protein? Thanks for your kind help! Sincerely, Xiang

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ADP refinement of cysteinesulfonic acid
by Phillip Steindel 17 Jul '13

17 Jul '13

Hi all- I have a 1.5 Angstrom structure with two cysteines that appear to have oxidized to cysteinesulfonic acid (OCS). I replaced the cysteines in coot, then ran refine with individual and anisotropic ADPs, but the ADPs don't appear to be refining for those residues. The hydrogens are all at 24,and the non-hydrogens are all at 20. I'm running 1.8.2-1309. Thanks, Phillip Steindel Theobald Lab Brandeis University

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cis peptide question
by Edward A. Berry 16 Jul '13

16 Jul '13

I have a cis-peptide in my structure. Phenix recognizes it and .geo file shows this is restrained to 0*: dihedral pdb=" CA ALA A 401 " pdb=" C ALA A 401 " pdb=" N SER A 402 " pdb=" CA SER A 402 " ideal model delta harmonic sigma weight residual 0.00 -1.58 1.58 0 5.00e+00 4.00e-02 1.00e-01 However in statistics printed with the output pdb, I have at least one dihedral that is flagged as off by about 180*: REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD MAX COUNT REMARK 3 DIHEDRAL : 12.902 168.987 3277 ^^^^^^^ Could this be my cis peptide, or do I have a really bad dihedral somewhere else?

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How do I turn off sidechain rotamer fitting?
by Owen Pornillos 16 Jul '13

16 Jul '13

I'm using one of the nightlies - dev 1427. It's not doing very well in combination with NCS. Or what is the most recent nightly that does not have this feature? Many thanks, Owen

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Kicked difference maps
by Ho Leung Ng 13 Jul '13

13 Jul '13

Hi, I am finding that features in kicked difference maps (mFo-DFc) have very different scaling compared to the standard difference maps. For example, a blob that appears in the standard map at 3 sigma might not appear in the kicked map until 5.5 sigma. Is this correct functioning? In contrast, features in the kicked and standard 2mFo-DFc maps are comparable in scale. Thank you, Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry hng(a)hawaii.edu

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problem with alternate conformations
by George Phillips 11 Jul '13

11 Jul '13

I am trying to adapt my old CNS scripts to to multiple conformer refinements in Phenix, i.e. up to 20 copies of each entire chain. I seem to be OK with up to three copies of the whole chain, but when I try four or more I seem to be in an infinite loop in the 'reduce' phase of a refinement. 3 copies runs in less than hour, even with torsion simulated annealing, with four even overnight the program just runs 'reduce for hours and hours'. This happens on the standard release and development version 1422. Is there some way to turn off hydrogens as a work around? Test files available on request. : ) Thanks for any help! George George N. Phillips, Jr. Ralph and Dorothy Looney Professor Department of Biochemistry and Cell Biology Rice University, MS140 6100 Main Street Houston, Texas 77005-1892 Office: +1 713.348.6951 http://www.bioc.rice.edu/

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2014 Gordon Research Conference and Research Seminars on Diffraction Methods in Structural Biology
by Anastassis Perrakis 11 Jul '13

11 Jul '13

Dear all, In a bit more than a year from now, we will be running the Gordon Research Conference on Diffraction Methods in Structural Biology, this time preceded for the first time by a two-day Gordon Research Seminar, exclusively for young scientists and a few mentors. http://www.grc.org/programs.aspx?year=2014&program=diffrac http://www.grc.org/programs.aspx?year=2014&program=grs_diff We are in the process of inviting the right people to make the schedule as exciting and inviting as possible, hoping we will be able to attract a diverse, enthusiastic, and motivated crowd! At this stage, we would like to ask you for ideas for 1. Specific subjects that are emerging and you would like to see covered, to make it worth your time to join us! 2. Specific people that would be excellent speakers, that would make you attend the Research Conference! 3. Specific people that would be great mentors, that would make you attend the Research Seminars! Many thanks from the team (but please send all replied to me!) Tassos Perrakis (GRC chair), Eddie Snell (GRC vice chair), Jeff Headd (GRS chair) and Maike Bublitz (GRS assoc. chair)

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parallel phenix.phaser on SGE cluster
by L. Costenaro (IBB) 11 Jul '13

11 Jul '13

Hello, I am trying to run phaser in a SGE cluster (qsub) using multiple proc (either phenix.phaser from the command line or phaser-MR from the GUI), but the jobs do not parallelize. When I run the phaser-MR locally (same executable) it does parallelize (multiple python threads). Any help , advice would be welcome. Best regards, Lionel

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Location of Gaussian factors for ED calculation
by Schubert, Carsten [JRDUS] 11 Jul '13

11 Jul '13

Hi, Were in the phenix package can I find the Gaussian factors (scattering table) for calculating the isotropic ED distribution at a given radius of r. I just need that for an illustration. Even better of you could already point me to some plots. Nothing I found online so far was suitable. Thanks Carsten

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: Post-doctoral position in structural biology (Paris, France)
by Benas Philippe 10 Jul '13

10 Jul '13

POST-DOCTORAL POSITION IN STRUCTURAL BIOLOGY (PARIS, FRANCE) . A postdoctoral position is available in the group of Dr. Carine Tisne at the Laboratory of Biological Crystallography and NMR of the University Paris Descartes, jointly with the group of Dr. Ciaran Condon at the Laboratory of Microbial Gene Expression (CNRS UPR9073) of the Institut de Biologie Physico-Chimique. We are studying the structure, function and folding of RNA and their complexes using NMR spectroscopy and X-ray crystallography, together with complementary biophysical methods. The postdoctoral research project focusses on the processing of the 5 and 3 ends of 5S rRNA in Gram-positive bacteria using solution NMR and X-ray crystallography as the main techniques. An integral part of our projects is the use and development of state-of-the-art preparative, biochemical and NMR techniques. . Interested candidates should hold a Ph.D. in Biochemistry, Biophysics or Structural Biology. Expertise in NMR spectroscopy and/or X-ray crystallography is mandatory. The successful candidate should be highly motivated, creative and capable of independent research in a two-team environment (10 minute walk between labs). The position is for a two-year term contract (one year in each team). We offer an exciting and enthusiastic work environment together with a stimulating location at the center of Paris (close to Jardin du Luxembourg). Facilities for structural biology include 600 MHz Bruker spectrometer equipped with cryoprobe. A new 700 MHz spectrometer will be installed in 2014. We also have access to high-field NMR spectrometers through the French TGIR and regular access to synchroton beamtime at either the ESRF or SOLEIL as Beam Time Allocation Group member. The ideal start date for the position would be October 2013. . Applications and informal queries about the labs and research projects should be directed by email to Carine Tisne (carine.tisne(a)parisdescartes.fr) or Ciaran Condon (condon(a)ibpc.fr[1]). Applications must include a letter of motivation summarizing current and future research interests, a CV, list of publications and letters of recommendation from at least two references. . ------------------------- PHILIPPE BENAS, PH.D. X-ray diffraction and computing facilities manager Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS E-mails: philippe.benas(a)parisdescartes.fr, philippe_benas(a)yahoo.fr URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18 ------------------------- "We do know nothing ! But tomorrow is another day ! ;-) " Liens: ------ [1] mailto:[email protected]

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give-up-quick Phaser in Rosetta
by Morten Grøftehauge 10 Jul '13

10 Jul '13

Dear Phenixbb, I was wondering if there was any way of getting Rosetta to give up easily and move on to another search model? Say I have 20 or more equally awful search models. I think there's a possibility that one of them will knock it out of the park (i.e. TFZ > 8). But even if I have Phaser set to fast search I will end up with an exhaustive search because the search models are so bad. fast_search_mode= True Run phaser with selection_criteria_rot_value and then if no obvious solution, repeat with cutoff lowered by search_down_percent search_down_percent= 25 Used if fast_search_mode=True. Run phaser with selection_criteria_rot_value and then if no obvious solution, repeat with cutoff lowered by search_down_percent If I set search_down_percent to 75 does this mean that Phaser will give up easily and move on to the next model? Is this a terrible strategy CPU-time-wise? I am of course aware that search_down_percent is much more likely to give me the right solution for a given model but in this case there are just so many possible search models. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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inconsistent Rwork/Rfree in outputs
by Michael Thompson 10 Jul '13

10 Jul '13

Hello All, I am getting an output from phenix.refine that is somewhat confusing to me. I have a log file that seems to be reporting inconsistent values for the final Rwork and Rfree. The last line of my log file says: Final R-work = 0.1815, R-free = 0.1912 However, when I check the pdb file from phenix.refine, I see: REMARK Final: r_work = 0.1799 r_free = 0.1952 bonds = 0.012 angles = 1.315 In the log file, I get the following table, which seems to agree with what is in the pdb file. R-factors, x-ray target values and norm of gradient of x-ray target stage r-work r-free xray_target_w xray_target_t 0 : 0.1971 0.1916 1.408780e-01 1.965297e-01 1_bss: 0.1971 0.1916 1.508155e-01 2.122150e-01 1_ohs: 0.1971 0.1916 1.447084e-01 2.026856e-01 1_xyz: 0.1928 0.2001 1.348543e-01 2.162596e-01 1_adp: 0.1929 0.2134 1.006068e-01 1.652532e-01 1_occ: 0.1928 0.2127 9.708801e-02 1.642701e-01 2_bss: 0.1784 0.1978 1.001979e-01 1.536656e-01 2_ohs: 0.1786 0.1982 1.146147e-01 1.876601e-01 2_xyz: 0.1777 0.1959 1.187570e-01 1.899659e-01 2_adp: 0.1952 0.2001 1.109064e-01 1.588435e-01 2_occ: 0.1952 0.1995 1.059382e-01 1.580417e-01 3_bss: 0.1831 0.1888 1.066004e-01 1.508888e-01 3_ohs: 0.1833 0.1890 1.217008e-01 1.855605e-01 3_xyz: 0.1824 0.1897 1.256200e-01 1.855714e-01 3_adp: 0.1876 0.2039 1.027854e-01 1.533022e-01 3_occ: 0.1877 0.2042 9.739524e-02 1.525993e-01 4_bss: 0.1770 0.1931 9.830779e-02 1.515598e-01 4_ohs: 0.1772 0.1933 1.132096e-01 1.824877e-01 4_xyz: 0.1775 0.1933 1.179076e-01 1.860704e-01 4_adp: 0.1911 0.2005 1.074584e-01 1.546149e-01 4_occ: 0.1909 0.1997 1.023003e-01 1.530269e-01 5_bss: 0.1805 0.1895 1.034638e-01 1.506407e-01 5_ohs: 0.1807 0.1895 1.185810e-01 1.828381e-01 5_xyz: 0.1803 0.1899 1.244219e-01 1.801964e-01 5_adp: 0.1893 0.2019 1.072974e-01 1.503622e-01 5_occ: 0.1893 0.2023 1.016701e-01 1.492730e-01 6_bss: 0.1792 0.1915 1.021896e-01 1.490341e-01 6_ohs: 0.1794 0.1915 1.174694e-01 1.798680e-01 6_xyz: 0.1804 0.1926 1.224254e-01 1.830383e-01 6_adp: 0.1952 0.2015 1.118187e-01 1.549205e-01 6_occ: 0.1950 0.2017 1.063759e-01 1.538692e-01 7_bss: 0.1842 0.1922 1.076805e-01 1.529198e-01 7_ohs: 0.1845 0.1918 1.227818e-01 1.857086e-01 7_xyz: 0.1846 0.1917 1.292627e-01 1.856928e-01 7_adp: 0.1885 0.2042 1.071531e-01 1.532154e-01 7_occ: 0.1885 0.2044 1.012764e-01 1.524448e-01 7_bss: 0.1797 0.1952 1.353649e-01 1.556126e-01 7_ohs: 0.1799 0.1952 1.353649e-01 1.556126e-01 I'm wondering why this last line of the log file isn't consistent with the other values that are being reported for R/Rfree? Which numbers should I believe? Thanks, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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GUI admin issues
by Yarrow Madrona 09 Jul '13

09 Jul '13

Hello, I have a couple of GUI related questions 1. We recently moved all of our data from one hard drive to another. However, we do not know how to change the directory for all of our projects. The directory is similar but the hard drive is now called tp3home instead of tp2home. We found a .phenix directory that has a file with a list of projects and directories. We updated the directories but this did not make a difference in the GUI. 2. Is there a quick way to specify which ligand or amino acid to remove in the GUI with doing simmulated annealing or better to do manually? Thanks. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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Re: [phenixbb] omit map for protein-DNA complex
by Wei Shi 09 Jul '13

09 Jul '13

Hi guys, With the help of Tom and Nat, I fixed the errors in my pdb file and could generate the simulated annealing omit map for the protein-DNA complex structure! But when I opened resolve_composite_map.mtz and *_ed.pdb in Coot, I could only see one monomer of the protein in Coot. It should be two dimers of the protein plus two pieces of DNA. And when I opened the *_ed.pdb in pymol, it showed the right thing: two dimers of the protein plus two pieces of DNA. It seems that something in *_ed.pdb file is not recognized by Coot. I don't know whether any of you had this before and would have any suggestions for me. When I opened *_ed. pdb with text file and found out that the word "break" is used instead of "ter" between different chains, so I replaced all "break" with "ter", but this didn't help.... Thank you so much! Best, Wei On Wed, Jul 3, 2013 at 10:36 AM, Wei Shi <wei.shi118(a)gmail.com> wrote: > Hi Nat and Tom, > Thank you so much for your help! I don't know why those C7 atoms are > there.... I just added some nucleotides manually using coot to fit the > density. I am going to delete those C7 atoms in DA and see whether that > would help. Thank you guys so much! > > Best, > Wei > > On Tue, Jul 2, 2013 at 5:22 PM, Nathaniel Echols <nechols(a)lbl.gov> wrote: > >> Okay, this makes sense. Wei, are you trying to model methylated DNA, >> or are those C7 atoms there by accident? >> >> -Nat >> >> On Tue, Jul 2, 2013 at 12:11 PM, Terwilliger, Thomas C >> <terwilliger(a)lanl.gov> wrote: >> > Hi Nat, >> > I think it was the input file. Here is a little piece of it: >> > >> > ATOM 3157 P DA E 8 -56.682 44.723-118.292 1.00 37.45 >> P >> > ATOM 3158 C5' DA E 8 -54.313 44.743-117.204 1.00 40.32 >> C >> > ATOM 3159 O5' DA E 8 -55.729 44.807-117.015 1.00 38.38 >> O >> > ATOM 3160 C4' DA E 8 -53.551 44.795-115.886 1.00 35.58 >> C >> > ATOM 3161 O4' DA E 8 -53.433 46.172-115.429 1.00 32.68 >> O >> > ATOM 3162 C3' DA E 8 -54.164 44.027-114.709 1.00 30.30 >> C >> > ATOM 3163 O3' DA E 8 -53.117 43.597-113.848 1.00 30.92 >> O >> > ATOM 3164 C2' DA E 8 -54.997 45.106-114.029 1.00 18.46 >> C >> > ATOM 3165 C1' DA E 8 -53.974 46.233-114.120 1.00 19.87 >> C >> > ATOM 3166 N1 DA E 8 -52.933 50.956-112.506 1.00 4.27 >> N >> > ATOM 3167 C2 DA E 8 -52.179 49.849-112.633 1.00 5.31 >> C >> > ATOM 3168 N3 DA E 8 -52.515 48.630-113.069 1.00 3.59 >> N >> > ATOM 3169 C4 DA E 8 -53.816 48.619-113.401 1.00 5.26 >> C >> > ATOM 3170 C5 DA E 8 -54.722 49.662-113.344 1.00 5.31 >> C >> > ATOM 3171 C6 DA E 8 -54.237 50.894-112.863 1.00 4.84 >> C >> > ATOM 3172 N6 DA E 8 -55.010 51.981-112.750 1.00 5.38 >> N >> > ATOM 3173 C7 DA E 8 -56.909 56.086-110.227 1.00 2.18 >> C >> > ATOM 3174 N7 DA E 8 -55.973 49.258-113.789 1.00 6.11 >> N >> > ATOM 3175 C8 DA E 8 -55.803 47.992-114.102 1.00 7.27 >> C >> > ATOM 3176 N9 DA E 8 -54.525 47.556-113.888 1.00 8.54 >> N >> > ATOM 3177 OP1 DA E 8 -56.215 43.588-119.122 1.00 44.46 >> O >> > ATOM 3178 OP2 DA E 8 -58.094 44.785-117.853 1.00 32.00 >> O >> > >> > Notice the C7 that is not attached to anything and is not normally part >> of a DA nucleotide. >> > -Tom T >> > >> > On Jul 2, 2013, at 1:07 PM, Nathaniel Echols wrote: >> > >> >> On Tue, Jul 2, 2013 at 9:03 AM, Wei Shi <wei.shi118(a)gmail.com> wrote: >> >>> Below is the error message I got when I ran a plain refinement of the >> same >> >>> PDB file and data file. I also ran phenix.ready-set of the PDB file >> using >> >>> default setting (add hydrogen to model if absent, et al) and generate >> a >> >>> updated PDB file and ran refine again, but still got the same error >> message >> >>> as below: >> >> >> >> This sounds like a bug. Could you please email us off-list with the >> >> PDB file and any existing restraints? (We can fake the data for >> >> testing purposes.) >> >> >> >> -Nat >> > >> > >

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Re: [phenixbb] problem refining Fe-S cluster
by Edward A. Berry 06 Jul '13

06 Jul '13

Pavel Afonine wrote: > Hi Ed, > > it looks like occupancies and B-factors need to be refined and refined > until convergence. Also, if you apply any distance restraints for > clusters (restrain Fe-S distances) make sure these restraints are > correct. I've seen many cases like this and typically refining > occupancy/b-factors and making sure restraints are correct solves the > problem. I've never seen fixing specific parameters help and I can't > understand logic for doing this. > OK. I'm not giving any restraints for the cluster, it must be in the monomers library. I can get SF4.cif from CCP4 and set the weights for bonds/angles very low to let the density rule. But now I see the problem wasn't there a few rounds back, and the difference seems to be that I was using 3 macro_cyles instead of 1. Now I repeat exactly the same refinement both ways, seems to be it. So maybe an artifact of not refining to convergence. Odd though, because it was OK in the starting model, and I'm not asking for the B's to be reset initially to 20 or something. Problem seems to be solved by using the default 3 cycles, but in case anyone is interested, B-factors for Fe are pretty much unchanged after refining 3 cycles B-factors for the Fe's but not the S's, decrease by about 5.0 on refining 1 cycle. Overall and protein B-ave increase on refining 1 cycle Looking at the step by step changes, the first cycle out of 3 is not like the single cycle. This is dev-1420 version of phenix. R-factors refining 3 cycles REMARK R-factors, x-ray target values and norm of gradient of x-ray target REMARK stage r-work r-free xray_target_w xray_target_t REMARK 0 : 0.3205 0.3532 3.857969e+00 3.920754e+00 REMARK 1_bss: 0.2433 0.2823 3.683390e+00 3.779722e+00 REMARK 1_weight: 0.2433 0.2823 3.683390e+00 3.779722e+00 REMARK 1_xyzrec: 0.2457 0.2825 3.689060e+00 3.780966e+00 REMARK 1_adp: 0.2463 0.2823 3.690454e+00 3.780932e+00 REMARK 1_occ: 0.2463 0.2823 3.690455e+00 3.780936e+00 REMARK 2_bss: 0.2463 0.2823 3.690087e+00 3.780536e+00 REMARK 2_weight: 0.2463 0.2823 3.690087e+00 3.780536e+00 REMARK 2_xyzrec: 0.2439 0.2821 3.684528e+00 3.778960e+00 REMARK 2_adp: 0.2434 0.2823 3.683429e+00 3.779315e+00 REMARK 2_occ: 0.2434 0.2823 3.683429e+00 3.779316e+00 REMARK 3_bss: 0.2433 0.2825 3.683615e+00 3.779760e+00 REMARK 3_weight: 0.2433 0.2825 3.683615e+00 3.779760e+00 REMARK 3_xyzrec: 0.2455 0.2825 3.688717e+00 3.780899e+00 REMARK 3_adp: 0.2461 0.2824 3.689934e+00 3.780715e+00 REMARK 3_occ: 0.2461 0.2824 3.689934e+00 3.780714e+00 REMARK end: 0.2457 0.2825 3.689963e+00 3.781089e+00 refining 1 cycle REMARK stage r-work r-free xray_target_w xray_target_t REMARK 0 : 0.3205 0.3532 3.857969e+00 3.920754e+00 REMARK 1_bss: 0.2222 0.2930 3.668217e+00 3.804573e+00 REMARK 1_weight: 0.2222 0.2930 3.668217e+00 3.804573e+00 REMARK 1_xyzrec: 0.2284 0.2941 3.681902e+00 3.808504e+00 REMARK 1_adp: 0.2594 0.3133 3.748285e+00 3.841014e+00 REMARK 1_occ: 0.2594 0.3133 3.748284e+00 3.841012e+00 REMARK end: 0.2692 0.2912 3.759155e+00 3.806820e+00 REMARK ------------------------------------------------------------------------ R B-factors refining 3 cycles REMARK |-----overall-----|---macromolecule----|------solvent-------| REMARK stage b_max b_min b_ave b_max b_min b_ave b_max b_min b_ave REMARK 0 : 90.34 16.23 43.10 90.34 16.23 42.91 80.33 27.29 46.57 REMARK 1_bss: 90.40 16.29 43.15 90.40 16.29 42.97 80.39 27.35 46.63 REMARK 1_weight: 90.40 16.29 43.15 90.40 16.29 42.97 80.39 27.35 46.63 REMARK 1_xyzrec: 90.40 16.29 43.15 90.40 16.29 42.97 80.39 27.35 46.63 REMARK 1_adp: 89.27 16.38 42.96 89.27 16.38 42.79 80.39 26.98 46.24 REMARK 1_occ: 89.27 16.38 42.96 89.27 16.38 42.79 80.39 26.98 46.24 REMARK 2_bss: 89.37 16.47 43.06 89.37 16.47 42.88 80.49 27.08 46.34 REMARK 2_weight: 89.37 16.47 43.06 89.37 16.47 42.88 80.49 27.08 46.34 REMARK 2_xyzrec: 89.37 16.47 43.06 89.37 16.47 42.88 80.49 27.08 46.34 REMARK 2_adp: 89.46 16.19 42.92 89.46 16.19 42.74 80.48 26.86 46.22 REMARK 2_occ: 89.46 16.19 42.92 89.46 16.19 42.74 80.48 26.86 46.22 REMARK 3_bss: 89.63 16.36 43.09 89.63 16.36 42.92 80.66 27.03 46.39 REMARK 3_weight: 89.63 16.36 43.09 89.63 16.36 42.92 80.66 27.03 46.39 REMARK 3_xyzrec: 89.63 16.36 43.09 89.63 16.36 42.92 80.66 27.03 46.39 REMARK 3_adp: 89.22 16.53 42.92 89.22 16.53 42.75 80.45 26.77 46.08 REMARK 3_occ: 89.22 16.53 42.92 89.22 16.53 42.75 80.45 26.77 46.08 REMARK end: 89.22 16.53 42.92 89.22 16.53 42.75 80.45 26.77 46.08 refining 1 cycle: REMARK |-----overall-----|---macromolecule----|------solvent-------| REMARK stage b_max b_min b_ave b_max b_min b_ave b_max b_min b_ave REMARK 0 : 90.34 16.23 43.10 90.34 16.23 42.91 80.33 27.29 46.57 REMARK 1_bss: 90.40 16.29 43.15 90.40 16.29 42.97 80.39 27.35 46.63 REMARK 1_weight: 90.40 16.29 43.15 90.40 16.29 42.97 80.39 27.35 46.63 REMARK 1_xyzrec: 90.40 16.29 43.15 90.40 16.29 42.97 80.39 27.35 46.63 REMARK 1_adp: 85.40 23.38 49.20 85.40 23.38 49.17 81.25 33.88 49.84 REMARK 1_occ: 85.40 23.38 49.20 85.40 23.38 49.17 81.25 33.88 49.84 REMARK end: 85.40 23.38 49.20 85.40 23.38 49.17 81.25 33.88 49.84 REMARK ------------------------------------------------------------------------ R starting model oswego 236% grep SF4 sqr1402e_002.pdb ATOM 8568 FE4 SF4 B1003 15.699 21.265 101.440 1.00 31.53 Fe ATOM 8569 FE1 SF4 B1003 15.302 20.444 104.268 1.00 28.32 Fe ATOM 8570 FE3 SF4 B1003 15.072 18.385 101.975 1.00 30.57 Fe ATOM 8571 FE2 SF4 B1003 17.702 19.420 102.964 1.00 32.57 Fe ATOM 8572 S2 SF4 B1003 14.066 20.264 102.463 1.00 39.50 S ATOM 8573 S3 SF4 B1003 16.963 21.440 103.248 1.00 28.46 S ATOM 8574 S1 SF4 B1003 16.723 19.393 100.994 1.00 31.08 S ATOM 8575 S4 SF4 B1003 16.026 18.425 103.963 1.00 29.56 S refining 3 cycles oswego 235% grep SF4 sqr1402e_006.pdb ATOM 8568 FE4 SF4 B1003 15.708 21.268 101.432 1.00 31.37 Fe ATOM 8569 FE1 SF4 B1003 15.283 20.449 104.291 1.00 28.14 Fe ATOM 8570 FE3 SF4 B1003 15.062 18.373 101.986 1.00 30.15 Fe ATOM 8571 FE2 SF4 B1003 17.720 19.419 102.961 1.00 32.34 Fe ATOM 8572 S2 SF4 B1003 14.080 20.264 102.462 1.00 38.64 S ATOM 8573 S3 SF4 B1003 16.943 21.422 103.257 1.00 28.96 S ATOM 8574 S1 SF4 B1003 16.712 19.383 101.004 1.00 31.27 S ATOM 8575 S4 SF4 B1003 16.036 18.446 103.959 1.00 29.32 S refining 1 cycle oswego 234% grep SF4 sqr1402e_005.pdb ATOM 8568 FE4 SF4 B1003 15.763 21.282 101.383 1.00 26.59 Fe ATOM 8569 FE1 SF4 B1003 15.274 20.434 104.305 1.00 23.38 Fe ATOM 8570 FE3 SF4 B1003 15.026 18.351 102.006 1.00 25.63 Fe ATOM 8571 FE2 SF4 B1003 17.779 19.437 102.902 1.00 27.63 Fe ATOM 8572 S2 SF4 B1003 14.132 20.305 102.437 1.00 34.56 S ATOM 8573 S3 SF4 B1003 16.929 21.408 103.255 1.00 28.42 S ATOM 8574 S1 SF4 B1003 16.681 19.335 101.002 1.00 29.49 S ATOM 8575 S4 SF4 B1003 16.105 18.462 103.923 1.00 28.25 S

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problem refining Fe-S cluster
by Edward A. Berry 05 Jul '13

05 Jul '13

I have a problem refining a structure with iron-sulfur clusters. The irons refine to low B-factors (~25 in this case, while wilson B and B-average are around 45 and the Sg's ligating the irons are ~30). The irons have negative difference density and there is positive density in the center of the cluster (not on the S as it appears; the S is actually above the plane of the irons and the positive density below). (see attached map) It's possible that the cluster is lost in some percent of the molecules, and I could refine occupancy to get rid of the negative density, but I suspect this is likely to be because the B-factors are too low. I will try manually setting B for the Fe's and refining without ADP step, but does anyone have a better suggestion? This was refined for one macrocycle with strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous thanks, eab

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divergence of R and Rfree at the last step of refinement
by Edward A. Berry 04 Jul '13

04 Jul '13

I'm refining a structure with phenix-dev-1414 version, and R-free decreases until the last step where R-work drops sharply and R-free increases. Am I doing something wrong? R-factors, x-ray target values and norm of gradient of x-ray target stage r-work r-free xray_target_w xray_target_t 0 : 0.3068 0.3347 4.111964e+00 4.184576e+00 1_bss: 0.2296 0.2735 3.919523e+00 4.036648e+00 1_weight: 0.2296 0.2735 3.919523e+00 4.036648e+00 1_xyzrec: 0.2377 0.2725 3.938818e+00 4.036514e+00 1_adp: 0.2311 0.2707 3.918953e+00 4.031556e+00 1_occ: 0.2311 0.2707 3.918944e+00 4.031541e+00 end: 0.2187 0.2795 3.907777e+00 4.050961e+00 ////////////////////////////////////////////////////////////////// Looking in the log file, it seems that this happens at the stage of correcting the solvent mask: ============================= updating all scales ============================= start: r_work=0.3152 r_free=0.3389 (reset all scales to undefined) bulk-solvent and scaling: r_work=0.2324 r_free=0.2703 remove outliers: r_work=0.2324 r_free=0.2703 *-> correct solvent mask: r_work=0.2187 r_free=0.2795 <--*** final: r_work=0.2187 r_free=0.2795 overall anisotropic scale matrix: V0: 2.5130,-0.3626,1.3424,-0.7174,-0.0625,-2.3276 V1: -0.0348,-0.0556,-0.0105,-0.0091,0.0085,0.0052

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Very low resolution data set
by Xiang Li 04 Jul '13

04 Jul '13

Hi everyone, I am working on a very low resolution data set (14 A). It is a designed DNA crystal and unit cell size & symmetry fit well with the assumption. When I do the refinement I found the Rfree is extreme high, ~0.49 while Rwork is about 0.4. But the model seems fits in well with the density map. I have collected different datasets, and it gives about the same MR result for different sets. I do not have any experience to work with low resolution data. Here I have a few questions: 1 What is the expected Rfree and Rwork for such low resolution data? I looked up PDB bank, and there is a 11.5A crystal with Rfree=~0.4. But not sure whether there is a kind of value for Rfree to consider the refinement works or not. 2 There might be overfit problem during the refinement. Currently what I did is to optimize the weight with PHENIX gui, add restraints between basepairs and NCS restraint. I tried to manually adjust the weight, but seems the optimized weight gives the best result. Are there other things I should try? 3 How to confirm that the result is real? There will be larger than usual error for such low resolution data, and what the supposed range should be? Thanks a lot for your suggestions and help! Sincerely, Xiang

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omit map for protein-DNA complex
by Wei Shi 03 Jul '13

03 Jul '13

Hi guys, I've been trying to generate the omit map for a protein-DNA complex structure using Phenix. I don't know why it takes forever to run and didn't seem like to finish at all.... The resolution of the dataset is 3.2A. Omit map type: simulated annealing. Omit region: composite. And, for the corresponding apo-protein structure, the simulated annealing omit map was generated within 2 or 3 hours on the same computer cluster. Let me know whether you have any idea about what might go wrong and whether there is anything I could do.... Thank you so much! Best, Wei

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Bias in Rfree
by "Weiergräber, Oliver H." 02 Jul '13

02 Jul '13

Hello, while refining a structure with NCS, I was re-considering this paper from Michael Chapman's group: Fabiola F, Korostelev A, Chapman MS. Bias in cross-validated free R factors: mitigation of the effects of non-crystallographic symmetry. Acta Crystallogr D Biol Crystallogr. 2006 Mar;62(Pt 3):227-38. In essence, they suggest to exclude from the working set reflections that are (1) related to a test reflection by NCS (2) adjacent to a test reflection and its NCS mates in reciprocal space They have implemented this strategy in a CNS module (R-free2005), but the software is no longer actively supported. Does anybody know if something similar has ever been implemented in other software packages such as phenix? Or am I missing any significant downsides of the approach - apart from a reduction of the working set? Best regards, Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Error while updating water
by Subhani Bandara 02 Jul '13

02 Jul '13

Dear all, I am refining a protein structure at 2.5 A. After running some refinements with water update option on, I manually added water to some positions and ran without water update option as it removes those water from the sites and show green density around. Then after some refinements like this, I tried to use water update option to add water to some newly appeared density. When I check the option to update water using dev 1418 version it stops with the following error. Also when not using water update option, refinement statistics got worse when I used 1418 compared to 1.8.2-1309 with refinements using same inputs and options. R work-0.1988 compared to 0.1920 with 1.8.2-1309 Rfree-0.2623 compared to 0.2490 with 1.8.2-1309 Traceback: File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/thread_utils.py", line 236, in run return_value = self._target(self._args, self._kwargs, self._c) File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/runtime_utils.py", line 94, in __call__ result = self.target() File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/runtime_utils.py", line 73, in __call__ result = self.run() File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/runtime.py", line 69, in run refine_object = self._run(args, callback) File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/runtime.py", line 85, in _run call_back_handler=callback) File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/command_line.py", line 161, in run call_back_handler=call_back_handler) File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/driver.py", line 1630, in run ncs_manager = self.ncs_manager).result File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/strategies.py", line 155, in __init__ neutron_refinement2 = self.neutron_refinement2) File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 26, in __init__ self.__call__() File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 36, in __call__ self.__getattribute__(method_name)() File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 106, in run_sol mc = self.macro_cycle) File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 79, in _need_to_run else: raise RuntimeError("Not a valid mode: %s"%mode) Thanks in advance for any help Subhani

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automatic weight optimization
by Michael Thompson 01 Jul '13

01 Jul '13

Hello Phenix Folks, I have a few questions about the automatic weight optimization in phenix.refine. I have read the manual, but I feel like maybe I'm missing something. I apologize in advance if these are naive questions, but here goes. I ran phenix.refine with a .def file, in which I set the following parameters: target_weights { optimize_xyz_weight = True optimize_adp_weight = True wxu_scale = 2.72 } My goal was to optimize both xyz and adp weights. In the log file, I see something like this: ===================== xyz refinement (lbfgs minimization) ===================== R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT TARGETS work free delta bonds angl data restr 21.06 20.38 -0.67 0.033 2.0 6.1 0.0 6.6 0 none 0.154 0.1685 19.79 21.26 1.47 0.012 1.3 7.6 0.0 5.8 0 2.494 0.131 0.0499 Legend: - first line corresponds to starting state (before refinement) - R-factors reported in percent - delta is Rfree-Rwork in percent - CLASH is all-atom Molprobity clashscore - ROTA is percent of side-chain rotamer outliers - RAMA is percent of Ramachandran plot outliers - CBET is number of Cbeta deviations - WEIGHT is relative weight between X-ray (or neutron) target and restraints - TARGETS: the values of X-ray (or neutron) and restraints target functions ================================ ADP refinement =============================== ----------Individual ADP refinement---------- R-FACTORS <Bi-Bj> <B> WEIGHT TARGETS work free delta data restr 19.79 21.26 1.47 1.909 20.062 0.661 0.131 19.80 21.28 1.49 1.761 20.011 0.007 0.130 19.77 21.41 1.64 1.838 19.884 0.030 0.125 20.30 22.63 2.34 2.369 19.168 0.122 0.111 20.17 22.82 2.64 2.886 18.929 0.243 0.107 20.07 23.04 2.97 3.771 18.737 0.365 0.104 20.04 23.14 3.10 4.106 18.751 0.486 0.103 20.00 23.19 3.19 4.496 18.794 0.608 0.103 19.98 23.23 3.25 4.846 18.851 0.729 0.102 19.97 23.27 3.29 5.115 18.940 0.851 0.102 19.95 23.30 3.36 5.420 18.988 0.972 0.101 19.94 23.33 3.39 5.579 19.008 1.094 0.101 19.93 23.29 3.36 5.598 18.917 1.215 0.101 max suggested <Bi-Bj> for this run: 10.00 max allowed Rfree-Rwork gap: 5.0 range of equivalent Rfree: 0.0 Best ADP weight: 0.007 Accepted refinement result: 19.80 21.28 1.49 1.761 20.011 0.007 0.130 The output kind of makes me feel like the adp weight is being optimized, but the xyz weight might not be. There is a list of statistics for varying values of the adp weight, but there is no similar list in the output from the xyz refinement stages. So my questions are: Is the xyz weight being optimized? Did I miss something in the input that is required to turn on xyz weight optimization? If the weight is indeed being optimized, then I must be misinterpreting the log file. How can I check to make sure the xyz weight optimization is running? Thanks for the help!! Mike Thompson -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

2 1

Format problem of restraint file
by Xiang Li 01 Jul '13

01 Jul '13

Hi everyone, I generated the basepairing restraint file by command phenix.secondary_structure_restraints MR.1.pdb > ss.eff . Then I opened the ss.eff file with gedit and edit the basepairing information. However, after I finished editing and saved the file, the refine program can not read the file. The error is "This application does not support the file type for ss.eff (format:txt)". I have attached a copy of the eff file. Do I have a way to solve the problem? Thanks for your help! Sincerely, Xiang

3 2

unwanted disulfids and geometry restraints
by Ursula Schulze-Gahmen 30 Jun '13

30 Jun '13

I have 2 questions: 1) I am using phenix.refine on the command line with a .eff file as input that was modified from previous GUI phenix runs. My structure has several Zn atoms and readyset creates a geometry_restraints file for the Zn interactions. I am not sure if phenix.refine gets these restraints when I run it from the command line. Do I need to read this file in some specific way? 2) The other question is: phenix refines several of the Cysteine neighbors in the Zn environment as disulfids, but they are not. How do I prevent this from happening? Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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Re: [phenixbb] what about heavy atom as model for MR
by zhaoy 30 Jun '13

30 Jun '13

Hi, It's my pleasure to recieved so much wonderful advice and I am trying according to the suggestions. I have used phenix.explore_metric_symmetry to see if there is any relationship between tetragonal and orthorhombic lattices. But the result suggests there is no relationship. In addition, I have some questions about the molecular replacement when density map entered as model. How to define clash between the model and How the value of RMS error of the density model impact the final MR result? Thank you! -- Yan Zhao, M.Phil. National Laboratory of Protein Sciences Institute of Biophysics Chinese Academy of Sciences 15 Datun Rd. Beijing, 100101 China Randy Read 写: Sorry, I'm coming a bit late to this thread, and most things I would have suggested have already been covered by Tom and Paul. Certainly there are examples in the literature of people using MR to place a heavy atom substructure against the anomalous differences, but as Tom pointed out there's the complication of making sure that you get the Se sites from one molecule and not from a combination of symmetry-related molecules, which probably won't have the same relative arrangement in the other crystal form. The one remaining thing I'd like to explore is whether you're sure that you've carried out the molecular replacement with density properly. This has become easier (with Tom's phenix.cut_out_density program), but it's still relatively complicated and error-prone. First, you have to be sure that you've cut out the density essentially for one molecule, and not a mixture of symmetry-related molecules. If the location and rough shape of the molecule isn't clear in your map, you may have to try things like cutting out spheres of density from different places in the unit cell and seeing which gives the clearest MR solution. Second, you have to make sure that you place the density in a reasonably large unit cell, 2.5-4 times the extent of the density that you've cut out, before using it as an MR model. Third, you have to choose an appropriate value for the effective RMS error of the density model. If your phases go to 4A, then a number like 1.5A to 2A might be appropriate. In our tests, the map can be pretty noisy but you can still get a very clear signal from the MR search. Of course, if the phase information is very weak, it still may not work even with an optimal envelope. Best wishes, Randy Read On 23 Jun 2013, at 15:56, "Terwilliger, Thomas C" <terwilliger(a)lanl.gov> wrote: You could try both the isomorphous and the anomalous differences. Each one has some useful information. You can even combine them but I'm guessing it won't help too much. Paul Adams' suggestion to check out related space groups is a very good one. Phenix.autosol only tries the opposite hand, so you have to try all the different screw axis possibilities that are not related by inversion. Another thing you could try is to repeat your MR with density from your map ( against the 2.6 A native) and get a long list of solutions. For each solution take the phases after MR and use them to calculate an anomalous difference Fourier for your semet P2221 data. Then notice if there are peaks in this map, and whether these peaks have the same relationship to the MR-placed density as you saw in your original map. If yes, you may have a solution. All the best, Tom T From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of zhaoy [zhaoy(a)moon.ibp.ac.cn] Sent: Sunday, June 23, 2013 3:32 PM To: PHENIX user mailing list Subject: Re: [phenixbb] what about heavy atom as model for MR Thank you very much. I will try as you said. The P2221 dataset's qulity are not very well. The points from diffraction image are not sharp. Besides, native dataset is 2.6A, setmet anomalous datasets is only 4A. So I have not obtained the solution with p2221datasets. There is only one molecular per AUS at p4322. So, from the initial map, I can confirm the heavy atom sites from the same molecular. Maybe I have a general idea about the method you said. But I still puzzled which F difference should I use, isomorphous or anomalous differences? Thanks! -- Yan Zhao, M.Phil. National Laboratory of Protein Sciences Institute of Biophysics Chinese Academy of Sciences 15 Datun Rd. Beijing, 100101 China Terwilliger, Thomas C 写: I'm not sure if there is a tool that will create the file you want for this. You could however just write a little script that reads in a .sca file and calculates F from I, subtract F+ - F- to get Dano, square that, write out Dano** 2 and sigma(Dano**2) as another .sca file. Then you could use this as input to molecular replacement with your sites from the P4322 dataset. There is an important caveat to this approach however: your sites from the P4322 have to be all part of the same molecule, and this might or might not happen automatically. If some sites are from one molecule and others from another molecule, then in the other crystal form their relationship won't be correct. If there is only one molecule in the au then this might or might not be a big problem. If there are more than one it is very likely to be a big problem. This would apply to the density search that you carried out as well. If your density is good enough to see where the molecule is, you might be able to figure out which of the symmetry-related sites to include in your MR search. Nevertheless as this is easy it seems like a fine thing to do. However I am wondering if it will work because your 2.6 A semet anomalous dataset did not yield a solution by itself, which is a little surprising... Also of course if your P4322 solution is not actually right or even just not close enough it would not work. -Tom T From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of 赵岩 [zhaoy(a)moon.ibp.ac.cn] Sent: Sunday, June 23, 2013 7:52 AM To: phenixbb(a)phenix-online.org Subject: [phenixbb] what about heavy atom as model for MR Hi everyone, The heavy atoms(Se-Met) were located at P4322 space group(4A). But the initial density map is so bad that I can not build the initial model. Meanwhile, I have another two datasets, native(2.6A) and se-met anomalous dataset with space group P2221. But these two datasets have no solution. I have tried the initial map from sp P4322 as a model to do molecular replacement. But no MR solution. So, I want to know how can I use the heavy atom as model to do MR with isomorphous or anomalous differences? Thanks! -- Yan Zhao, M.Phil. National Laboratory of Protein Sciences Institute of Biophysics Chinese Academy of Sciences 15 Datun Rd. Beijing, 100101 China _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Is DEN refinement working?
by Wallen, Jamie 29 Jun '13

29 Jun '13

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PHASER-TFZ scores with ensembles higher?
by Jan Gebauer 28 Jun '13

28 Jun '13

Dear Phaser users, I recently tried to solve two difficult MR jobs by using ensembles in PHASER. With ENSEMBLES in this case I mean aligned structures prepared for PHASER by Phenix.ENSEMBLER. In both case I got solution with rather high TFZ-score (> 8), which I couldn't get wit individual structure, but was not able to refine them. My question is, whether using ensembles would increase the Z-Score without really improving phases. In other words, if there is another cut-off for the "Phaser solved it" Z-score, when using ensemble in contrast to single structures... Regards, Jan -- Dr. Jan Gebauer AG Prof. Baumann Institut für Biochemie / Uni-Köln Otto-Fischer-Str. 12-14 / 50674 Köln Fon: +49 (221) 470 3212 Fax: +49 (221) 470 5066 http://px.uni-koeln.de/

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refining the anomalous Se in MSE using Phenix Gui
by Kenneth A. Satyshur 28 Jun '13

28 Jun '13

Sirs: I am trying to refine the anomalous data in phenix refine. I am using the GUI and I get a box for the anomalous groups. But I when I put in 'Se' and refine: phenix says 'Sorry'. If I use View, I get all atoms in a viewer. I have 5 molecules of 330 residues each and 25 total Se atoms. I cannot possibly pick them out from the molecular display. Then I tried to make a heavy atom file with just selenium in it, but on input, it is read as a 'input model' and when I refine, it says 'duplicate atoms'. Without the anomalous refine, there is a lot of residual Fo-Fc density around the seleniums in the maps. How do I enter the 'anomalous group' into phenix refine. What is the syntax? I can find no help file or documentation on this. Anyone done this before? thanks -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207

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Phenix version 1.8.2 released
by Paul Adams 26 Jun '13

26 Jun '13

The Phenix developers are pleased to announce that version 1.8.2 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Highlights from this version: Ensemble refinement, updated hydrogen parameters in refinement and validation, mmCIF reading and writing, LLG maps output from refinement, ligand pipeline for automated solution of protein/ligand complexes, autobuilding starting from a very accurate but very small part of a model, CC* calculation from unmerged data, maximum entropy maps, and PDB editor. Graphical interface: ==================== - New GUIs: phenix.merging_statistics, phenix.pdb_editor General: ======== - Multiple bug fixes - phenix.refine, phenix.reduce, and MolProbity updated to use consistent, revised, electron-cloud centers for hydrogen positions as default (for X-ray) - also see MolProbity website for details: http://molprobity.biochem.duke.edu - mmCIF format now supported in place of PDB format for input to many programs - new commands: phenix.ensemble_refinement, phenix.ligand_pipeline, phenix.sort_hetatms, phenix.cc_star, phenix.pdb_editor, phenix.maximum_entropy_map Refinement: =========== - phenix.refine - support for LLG map type - uses Phaser to compute residual anomalous LLG map - best when used with group_anomalous strategy, which will flatten the LLG map around existing anomalous scatterers with refined f'/f''. - alternatively, anomalous_residual map type (similar but less sensitive) - automatic linking in refinement and pdbtools for residues in the same chain - enabled with automatic_linking.intra_chain=True; this includes carbohydrate linking to protein and between sugars, and covalently bound ligands. - optional output of mmCIF format model and data files - phenix.ensemble_refinement (new command): - New method for refining ensemble models - Combines MD simulation with X-ray restraints that simultaneously account for anisotopic and anharmonic atomic distributions. - For full description see: Burnley BT, Afonine PV, Adams PD, Gros P. 2012. Modelling dynamics in protein crystal structures by ensemble refinement. eLife 1:e00311. doi: 10.7554/elife.00311. Experimental Phasing and Model Building: ======================================== - phenix.autobuild: - now uses torsion NCS parameterization when NCS is used in refinement - building starting from a very accurate but very small part of a model: You can now use the keyword rebuild_from_fragments=True to start rebuilding from fragments of a model. You might want to use this if you look for ideal helices using Phaser, then rebuild the resulting partial model, as in the Arcimboldo procedure. The special feature of finding helices is that they can be very accurately placed in some cases. This really helps the subsequent rebuilding. If you have enough computer time, then run it several or even many times with different values of i_ran_seed. Each time you'll get a slightly different result. - Base-pairing in RNA building -- phenix.autobuild will now try to guess which bases in a model are base-paired, and if there is no positive sequence match to the model, the bases that are base-paired will be chosen to be complementary. You can set the cutoff for base pairing with the keyword dist_cut_base. - waters are automatically named with the chain of the closest macromolecule if you set sort_hetatms=True. This is for the final model only. - you can supply a target position for your model with map_to_object=my_target.pdb. Then at the very end of the run your molecule will be placed as close to this as possible. The center of mass of the autobuild model will be superimposed on the center of mass of my_target.pdb using space group symmetry, taking any match closer than 15 A within 3 unit cells of the original position. The new file will be overall_best_mapped.pdb. Molecular Replacement: ====================== - phenix.mr_rosetta - You can now give commands for Rosetta in mr_rosetta, including a command to specify where disulfide bonds are located - The Rosetta models are now identified by an ID number so that they have unique names - Default number of homology models to download is now 1 (was 5) - Default number of NCS copies (if ncs_copies=Auto) is number leading to solvent content closest to 50%; if ncs_copies=None then all plausible values of ncs_copies are tested. New commands: ============= - phenix.ligand_pipeline (new command): - combines Xtriage, Phaser, eLBOW, phenix.refine, AutoBuild, and LigandFit to automatically solve protein/ligand complexes - optional integration with Coot (parameter interactive=True) allows semi-interactive operation where more rebuilding is required - phenix.cc_star (new command): - combined assessment of model and data quality, as outlined in Karplus & Diederichs (2012) Science 336:1030-3. - summary also output by phenix.model_vs_data if additional unmerged_data keyword is specified - phenix.maximum_entropy_map (new command): - tool to compute maximum entropy map from map coefficients. The program reads input Fourier map coefficients and modifies corresponding synthesis using Maximum-Entropy Method (MEM). The MEM modified map is everywhere positive, smooth and is of higher resolution. The method uses is a modification of Gull & Daniell (1978) algorithm. - phenix.sort_hetatms (new command): - rearranges heteroatoms (ligands, waters, etc.) in a model so they are paired with the nearest macromolecule chain, similar to the PDB's processing of models - phenix.pdb_editor (new command): - graphical editor for PDB files, based on tree view of model hierarchy - perform common operations such as chain renaming, renumbering, manipulation of atomic properties, add/remove atoms Ligands: ======== - phenix.ready_set: - methyl rotations now automatic when adding explicit hydrogens (also in phenix.reduce) - more options adding deuteriums to a model have been introduced Miscellaneous: ============== - phenix.xtriage: - include merging statistics if unmerged intensities are used as input - phenix.maps: - added wavelength parameter and support for anomalous residual and Phaser LLG map coefficients For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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what about heavy atom as model for MR
by 赵岩 26 Jun '13

26 Jun '13

Hi everyone, The heavy atoms(Se-Met) were located at P4322 space group(4A). But the initial density map is so bad that I can not build the initial model. Meanwhile, I have another two datasets, native(2.6A) and se-met anomalous dataset with space group P2221. But these two datasets have no solution. I have tried the initial map from sp P4322 as a model to do molecular replacement. But no MR solution. So, I want to know how can I use the heavy atom as model to do MR with isomorphous or anomalous differences? Thanks! -- Yan Zhao, M.Phil. National Laboratory of Protein Sciences Institute of Biophysics Chinese Academy of Sciences 15 Datun Rd. Beijing, 100101 China

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possible Xtriage bug??
by Michael Thompson 26 Jun '13

26 Jun '13

Hello Developers, I would like to report a possible bug in newer versions of phenix.xtriage. I have noticed recently that I am getting some strange results for the results of the L-test when I run xtriage, as described below: My data show a strong non-crystallographic translation, described by the vector <uvw>=(1/3, 2/3, 1/2). This NCS translation is readily identified by xtriage. When Xtriage performs the L-test, the output states: L test for acentric data using difference vectors (dh,dk,dl) of the form: (2hp,2kp,2lp) where hp, kp, and lp are random signed integers such that 2 <= |dh| + |dk| + |dl| <= 8 Mean |L| :0.504 (untwinned: 0.500; perfect twin: 0.375) Mean L^2 :0.340 (untwinned: 0.333; perfect twin: 0.200) These results don't make sense, as the statistics show an "anti-twinned" effect, which should not happen with the L-test. It appears that xtriage is using reflections that do not have the same expected intensity values due to the NCS translation. The strange thing is that I have another xtriage logfile, which I produced in September of 2012 using the same input data, that indicates the reflections used for the L-test were chosen "using difference vectors (dh,dk,dl) of the form: (3hp,3kp,2lp)." This choice of reflections does account for proper parity, and I get results that are much more sensible (Mean |L|=0.394; Mean L^2=0.221). I am wondering why I am getting different results now than I did last September? Has something changed in the underlying code, or am I missing something silly? I do not have an easy way of determining which version of phenix I used when the L-test was conducted using sensible reflections (the xtriage logfile doesn't contain this info as far as I can tell), but the version that seems to choose reflections inappropriately is 1.8.2-1334. Thanks a lot for the help, and for phenix being awesome in general! Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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How to treat EDTA on a special position
by Jan Gebauer 26 Jun '13

26 Jun '13

Dear all, I recently solved a structure in R32/H (155). Interestingly some crystal contacts are mediated by an Metal/EDTA complex. The metal -presumably a magnesium- sits on a special position (x,0, 1/2) in the middle of a twofold axis with the EDTA molecule coordinating it. (See "top" view in dropbox image below) If I fit the EDTA/Mg complex in the density, the symmetry will of course generate a symmetry mate on the same spot. (see "side" view in dropbox image below). In phenix.refine, both entities are refined, which of course gives wrongs results. My question is, how to best define the Ligand to be compatible with phenix.refine and -later- with pdb submission. Should I just set occupancy to 0.5 for the whole EDTA molecule? - But then I would still get two molecules at this site... Or split it somehow half and let the second half be generated by symmetry? In that case, I would need to define bonds over the asymmetric unit to prevent "dissociation" of my ligand halves, wouldn't I? Or is there a third way? I already searched the phenixBB, but only found some "old" threads discussing vaguely similar problems. Unfortunately, they didn't help me to answer which way is better... (or right...) Regards, Jan DROPBOX IMAGE: https://dl.dropboxusercontent.com/u/29745394/R32%20-%20EDTA.jpg -- Dr. Jan Gebauer AG Prof. Baumann Institut für Biochemie / Uni-Köln Otto-Fischer-Str. 12-14 / 50674 Köln Fon: +49 (221) 470 3212 Fax: +49 (221) 470 5066 http://px.uni-koeln.de/

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completeness in table1
by Alexander Batyuk 25 Jun '13

25 Jun '13

Dear developers, What could be the reason for discrepancy in completeness reported in XSCALE.LP (94.5% - 100.0%) vs from Table1: 89.57% (37.49%)? Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

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Re: [phenixbb] How to export difference patterson map in PHENIX
by Ulrich Baumann 20 Jun '13

20 Jun '13

Hi Nat I tried to limit the resolution by either --diff_limit 4 or --high_resolution 4.0. This does not work - probably is not supposed to work in this way? Thanks, ULrich lrich-Baumanns-iMac:xds_new ubaumann$ cctbx.patterson_map au1_run1_Rfree.mtz --high_resolution 4. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !! WARNING - EXPERIMENTAL PROGRAM !! !! !! !! This program is still in development - some functionality may be !! !! missing and/or untested. Use at your own risk! For bug reports, etc. !! !! email bugs(a)phenix-online.org. !! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Traceback (most recent call last): File "/usr/local/phenix-dev-1405/build/mac-intel-osx-x86_64/../../cctbx_project/iotbx/command_line/patterson_map.py", line 176, in <module> run(sys.argv[1:]) File "/usr/local/phenix-dev-1405/build/mac-intel-osx-x86_64/../../cctbx_project/iotbx/command_line/patterson_map.py", line 136, in run params = cmdline.work.extract() File "/usr/local/phenix-dev-1405/cctbx_project/libtbx/phil/__init__.py", line 1690, in extract value = object.extract(parent=result) File "/usr/local/phenix-dev-1405/cctbx_project/libtbx/phil/__init__.py", line 1086, in extract return self._type_from_words()(self.words, master=self) File "/usr/local/phenix-dev-1405/cctbx_project/libtbx/phil/__init__.py", line 320, in from_words value = self._value_from_words(words=words, path=master.full_path()) File "/usr/local/phenix-dev-1405/cctbx_project/libtbx/phil/__init__.py", line 348, in _value_from_words return float_from_words(words=words, path=path) File "/usr/local/phenix-dev-1405/cctbx_project/libtbx/phil/__init__.py", line 274, in float_from_words result = number_from_words(words=words, path=path) File "/usr/local/phenix-dev-1405/cctbx_project/libtbx/phil/__init__.py", line 227, in number_from_words value_string=str_from_words(words), words=words, path=path) File "/usr/local/phenix-dev-1405/cctbx_project/libtbx/phil/__init__.py", line 212, in number_from_value_string path, value_string, words[0].where_str())) RuntimeError: Error interpreting high_resolution="True" as a numeric expression (command line argument, line 1) Ulrich-Baumanns-iMac:xds_new ubaumann$ cctbx.patterson_map au1_run1_Rfree.mtz --diff_limit 4 ---------------------------------------- Prof. Ulrich Baumann, PhD Institute of Biochemistry, University of Cologne Otto-Fischer-Strasse 12-14, D-50674 Cologne, Germany

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X-ray/Neutron joint refinement
by Emily Golden 20 Jun '13

20 Jun '13

Hi All, I have a couple of questions about X-ray/neutron joint refinement in phenix. Is it possible to use the neutron data only for refining hydrogen atom positions and the X-ray data for all other atoms? I used the option to add hydrogen atoms to model and refine H/D at exchangable sites and H elsewhere. This worked for many of the exchangeable hydrogen atoms. However, for some side chains, especially Lysine, the program has placed a hydrogen and deuterium atom (with refined occupancies) in the same position as the atom it is supposed to be bonded to. Does anybody know why this is happening and what I may be able to do about it. Or will I need to manually move each misplaced H/D in Coot? Thank you for your help. Emily

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Jerry Karle
by Robert Sweet 19 Jun '13

19 Jun '13

Jerry Karle died a couple of weeks ago, and one of us here learned about it by noticing his obituary in the NY Times: http://www.nytimes.com/2013/06/15/health/jerome-karle-94-dies-nobelist-for-… He's well known to those of us who started in this field when the solving of a Patterson function for a heavy atom in a structure was the only way we knew to get the structure. With Herb Hauptman, and in close teamwork with his wife Isabella who actually >did< crystallography, he played a major role in working out the sort of Direct Methods that allowed one to solve ordinary small-molecule structures before the days of high-speed computing. As the obituary points out, Jerry and Herb shared the 1985 Nobel Prize in Chemistry for this work. The obit. is worth reading. I suspect you'll see an even better one in Nature soon. My own tiny personal memory of Jerry Karle: When I was a grad student at the Univ. of Wisc. with Larry Dahl I made a pilgrimage to the NRL to visit Jerry and Isabella. I was trying to use direct methods to solve at least one cephalosporin structure, which eventually appeared in my thesis, and there was a feature of DM that I failed to understand. They were very patient with me, but couldn't understand what it was I didn't get. It turns out to have been essentially trivial, but that's the way it goes sometimes. Anyway he always recognized me afterwards, or pretended to. I was delighted on arriving at BNL to discover that his daughter Louise was here. Bob ========================================================================= 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 Biosciences Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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