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bug report- gui freezed
by Kendall Nettles 04 Apr '11

04 Apr '11

The GUI freezes when an add dialog box is open and a job ends, launching an announcement box (..coot is starting, ready set is done...etc). I can't close either box. Using phenix-1.7-650 on a mac Kendall

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phenix.maps2mtz
by Yarrow Madrona 02 Apr '11

02 Apr '11

Hello, I am running phenix-1.7-650 and would like to generate a ccp4 map for use in pymol from an mtz. I can type: phenix.maps2mtz file.mtz but I cannot figure out how to limmit the selection to a single chain (chain A). I guess you can do this in maps.params but I wanted to keep it simple without having to use the sca file. Thank you. -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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"FOM" or HL coeffs from model?
by Phoebe Rice 01 Apr '11

01 Apr '11

How can I get phenix to spit out not just PhiModel but an estimated FOM or fake HL coefficients (without experimental phases - just based on how badly my model agrees with FOBS)? And I'd like the weights in their own personal mtz column(s), not just precombined in a "weighted phi" column. In case anybody cares why, I'd like to use solvent massaging and domain-wise averaging to remove bias from a low-resolution model-phased map, preferably with DM, unless anybody has a better suggestion. I did rigid body, TLS, etc on the model in phenix, so it seems like phenix has already calculated all the info I want if I could only squeeze it out. thanks, Phoebe ===================================== Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alph… http://www.rsc.org/shop/books/2008/9780854042722.asp

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phenix.reciprocal_space_arrays: a new command line tool to get Fcalc, Fbulk, Fmask, FOM, HL, and more all in one MTZ file
by Pavel Afonine 01 Apr '11

01 Apr '11

PHENIX users: just a quick notice: starting PHENIX nightly build version dev-717 and up, a new command line tool phenix.reciprocal_space_arrays will be available. This tool takes a PDB model and a data file (in most of commonly used formats: MTZ, CNS, SHELX,...) and outputs a MTZ file containing a number of arrays that are typically used in various crystallographic calculations, such as R-factors, maps, refinement targets, etc. The output arrays include: Fmodel, Fcalc, Fmask, Fbulk, FOM, resolution, HL(input original, computed from model and combined), FB_CART (overall anisotropic scale), input Fobs and Rfree-flags and more. To run: phenix.reciprocal_space_arrays model.pdb data.mtz To see the result: phenix.mtz.dump output_file.mtz Please let me know should you have any questions, suggestions or simply find a bug! Pavel.

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low resolution map weirdness with newer releases
by Scott Classen 01 Apr '11

01 Apr '11

Something changed between build 432 and 486 that made my low resolution maps look much crappier. See attached tiff. See if you can guess which map was produced by the release 486. def file looks more or less like this (from a --diff-params): refinement { crystal_symmetry { unit_cell = top secret space_group = top secret } input { pdb { file_name = "../4_23_003.pdb" } xray_data { file_name = "../4_23.sca.mtz" labels = "4_23.sca,SIG4_23.sca" high_resolution = 3.9 r_free_flags { file_name = "../4_23.sca.mtz" label = "R-free-flags" test_flag_value = 1 } } } output { prefix = "test-486" serial = 1 } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ individual_adp group_adp tls occupancies group_anomalous sites { individual = "chain A and resseq 100:107" individual = "chain B and resseq 500:507" individual = "chain E and resseq 100:107" individual = "chain F and resseq 500:507" individual = "chain C and resseq 111:117" individual = "chain D and resseq 111:117" individual = "chain G and resseq 111:117" individual = "chain H and resseq 111:117" individual = "chain C and resseq 63:68" individual = "chain D and resseq 63:68" individual = "chain G and resseq 63:68" individual = "chain H and resseq 63:68" rigid_body = "chain A" rigid_body = "chain B" rigid_body = "chain C" rigid_body = "chain D" rigid_body = "chain E" rigid_body = "chain F" rigid_body = "chain G" rigid_body = "chain H" } } main { number_of_macro_cycles = 1 secondary_structure_restraints = True random_seed = 3141766 optimize_mask = False } modify_start_model { adp { set_b_iso = 50 } } fake_f_obs { mask { ignore_hydrogens = True } } geometry_restraints.edits { excessive_bond_distance_limit = 20 } mask { ignore_hydrogens = True } simulated_annealing { start_temperature = 300 final_temperature = 200 } target_weights { wxc_scale = 0.4 } ias { b_iso_max = 60 } secondary_structure { h_bond_restraints { substitute_n_for_h = True remove_outliers = False sigma = 0.02 h_o_distance_ideal = 2.95 h_o_distance_max = 5 n_o_distance_ideal = 2.95 n_o_distance_max = 5 } }

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omit map
by intekhab alam 01 Apr '11

01 Apr '11

Hi i generated an iterative build omit map using phenix and the output fule that i got is resolve_composite_map.mtz, but i cannot open this file in coot, what modifications do ineed to open this file in coot. Regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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Bulk solvent correction
by Ina Lindemann 31 Mar '11

31 Mar '11

Hi, I am refining two crystal structures of the same protein wtih four domains and 687 amino acids. These are the last lines form my log-files after several model building steps - protein altogether fits quite well into the density. But I am confused about these logfiles: 1.Why is there such a big difference between R values with and without bulk solvent correction and anisotropic scale? Start R-work = 0.3765, R-free = 0.5498 (no bulk solvent and anisotropic scale) Final R-work = 0.3733, R-free = 0.5509 (no bulk solvent and anisotropic scale) Start R-work = 0.2356, R-free = 0.2962 Final R-work = 0.2250, R-free = 0.2939 2. (the other structure) Why does the R value without bulk solvent and anisotropic scale decrease so much but with it remains stable? Start R-work = 0.2182, R-free = 0.2856 (no bulk solvent and anisotropic scale) Final R-work = 0.4054, R-free = 0.4223 (no bulk solvent and anisotropic scale) Start R-work = 0.2157, R-free = 0.2827 Final R-work = 0.2147, R-free = 0.2816 I would be very pleased about any helpful comments. Ina Ina Lindemann Philipps-Universität Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908

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what to do with disordered side chains
by Ed Pozharski 31 Mar '11

31 Mar '11

The results of the online survey on what to do with disordered side chains (from total of 240 responses): Delete the atoms 43% Let refinement take care of it by inflating B-factors 41% Set occupancy to zero 12% Other 4% "Other" suggestions were: - Place atoms in most likely spot based on rotomer and contacts and indicate high positional sigmas on ATMSIG records - To invent refinement that will spread this residues over many rotamers as this is what actually happened - Delet the atoms but retain the original amino acid name - choose the most common rotamer (B-factors don't "inflate", they just rise slightly) - Depends. if the disordered region is unteresting, delete atoms. Otherwise, try to model it in one or more disordered model (and then state it clearly in the pdb file) - In case that no density is in the map, model several conformations of the missing segment and insert it into the PDB file with zero occupancies. It is equivalent what the NMR people do. - Model it in and compare the MD simulations with SAXS - I would assumne Dale Tronrod suggestion the best. Sigatm labels. - Let the refinement inflate B-factors, then set occupancy to zero in the last round. Thanks to all for participation, Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs

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phenix migration
by Xtal_bb 31 Mar '11

31 Mar '11

Hi guys, I have just got a brand new iMac, to replace my MacBook, in which I used to run phenix. I have installed phenix in the new iMac, and copied the directory with all the files of my previous runs. However, what should I migrate to have the projects and previous work recognized by the fresh install? Thanks for the help, ciao s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990

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how convert mtz in xplor format
by fulvio saccoccia 30 Mar '11

30 Mar '11

Greetings to all, Does anyone know how convert a .mtz file into a xplor format file? Thanks in advance Fulvio Saccoccia

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rotamers
by Ed Pozharski 29 Mar '11

29 Mar '11

Does refine restrains side chain rotamers to, say, the closest one from the rotamer dictionary or, perhaps, the starting coordinates (I find this less likely, of course)? I am particularly interested in what would happen if a side chain is disordered and there is no strong electron density to support a specific conformation. Do I understand correctly that the real-space refinement for the side chains is on by default, which means that disordered side chains would tend to stay within their biased density? I apologize if I missed the description of this in the manual, just point me to the right section then. Cheers, Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs

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are the rigid_body group shifts cummulative or stepwise?
by Scott Classen 29 Mar '11

29 Mar '11

i.e. do the translation & rotation values reported in each rigid body step in the log file represent the TOTAL shift from the initial pre-RB model or just the shift for that particular step? Thanks, Scott

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Same enzyme, different space groups ?
by Yuri 28 Mar '11

28 Mar '11

Hello everyone, I was comparing 2 data sets I have and when I run Xtriage I noticed the following: a) for one crystal (data processed in P 4 2 2) | space group | n absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- | score | ------------------------------------------------------------------------------------ | P 41 21 2 | 24 | 0.03 | 1.30 | 0 | 2 | 0.000e+00 | | P 43 21 2 | 24 | 0.03 | 1.30 | 0 | 2 | 0.000e+00 | | P 42 21 2 | 22 | 0.03 | 1.27 | 0 | 4 | 7.187e-02 | | P 4 21 2 | 18 | 0.01 | 1.21 | 0 | 8 | 3.035e-01 | | P 41 2 2 | 6 | 0.11 | 1.59 | 0 | 20 | 9.065e-01 | | P 43 2 2 | 6 | 0.11 | 1.59 | 0 | 20 | 9.065e-01 | | P 42 2 2 | 4 | 0.13 | 1.57 | 0 | 22 | 9.784e-01 | | P 4 2 2 | 0 | 0.00 | 0.00 | 0 | 26 | 1.210e+00 | ------------------------------------------------------------------------------------ b) the other crystal, of the same enzyme (data scaled in P 43 21 2) x triage tells me this crystal is in P 43 21 2. | space group | n absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- | score | ----------------------------------------------------------------------------------- | P 4 2 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 4 21 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 41 2 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 41 21 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 42 2 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 42 21 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 43 2 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 43 21 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | ----------------------------------------------------------------------------------- My understanding is that P 43 21 2 should have 0 systematic absences (if I am wrong, please point it out) My questions are: what is really my space group? Or should I say space groups, if indeed I have two different space groups. How do I nterpret the scores? Could it all be a function of the space group they were processed in? -- Yuri Pompeu

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Target weight optimization (wxu_scale and wxu)
by Zhang yu 28 Mar '11

28 Mar '11

Dear Phenixer, What is the real meaning of the 'wxu_scale' and 'wu'? (scale factor for X-ray/ADP_weight: wxu_scale ADP weight scale: wu) During ADP refinement, it is suggested to refine the 'wxu_scale', what if I change the value of 'wu'? Thanks Yu

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Split Occupancy of a ligand and water
by Brandon Goblirsch 28 Mar '11

28 Mar '11

Hello, Currently I am have a structure which has a ligand bound at less than full occupancy. The ligand in this cause is covalently linked to a CYS residue in the enzyme active site. When the ligand is not present, there are two well conserved waters in the active site in its place. Overall, I have a same space, split occupancy issue. The problem I am having now in phenix 1.7.460 is that I want to refine (simultaneously) these water positions superimposed on the bound ligand position (as both have less than 100% occupancy). However, upon refinement, the waters are always "kicked out" of position and are not allowed to overlay with atoms within the bound ligand. Does anyone know how to get phenix.refine to accept the water and ligands occupying the same coordinate space. Obviously setting the ligand and water positions to sub 100% occupancy does not do the trick. Thanks for any help!! Brandon -- Brandon Goblirsch Research Assistant-Wilmot Lab Biochemistry, Molecular Biology and Biophysics 5-230 Nils Hasselmo Hall Minneapolis, MN 55455 (612)624-0141

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anomalous difference map
by Jason 28 Mar '11

28 Mar '11

Hello Everyone, I have an old question about how to create anomalous difference map. Facts: 1) Synchrotron Fluorescence scan indicates the heavy atom definitely presents in my protein (my control is a second protein with the same ligand showed no absorbance spectrum) 2) xds processed mtz file 3) Data resolution ~ 3 angstron 3) molecular replacement solved apo structure protein.pdb using phenix.refine 4) phenix.maps to generate anomalous map (phenix.refine will also generate it, but let's leave it aside for the moment) Questions: When I load the mtz file to phenix.maps GUI, the mtz label pulldown menu indicates 4 possible choices for the column to use:(1) IMEAN, SIGIMEAN (2) I(+), sigI(+), I(-), sigI(-) merged (3) F(+), sigF(+), F(-), sigF(-) merged (4) F, sigF, Dano SigDano. I have tried the choices of (2) (3) and (4). However, there is barely any anomalous signal at 4sigma, which makes me wondering if something is not right. The first thing coming to my mind is the mtz labels: I(+), sigI(+), I(-), sigI(-) merged. What does merged mean? Could this be the reason? Other issues that could causing the trouble? Thank you all. ====================== Jason Structural Biology Department University of Pittsburgh ======================

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secondary structure restraints
by Bradley Hintze 28 Mar '11

28 Mar '11

Hello PHENIX developers. When I run phenix.secondary_structure_restraints 1ZY7.pdb format=refmac I get this error: Traceback (most recent call last): File "/Users/bradleyhintze/phenix/phenix-dev-699/cctbx_project/mmtbx/command_line/secondary_structure_restraints.py", line 6, in <module> secondary_structure.run(sys.argv[1:]) File "/Users/bradleyhintze/phenix/phenix-dev-699/cctbx_project/mmtbx/secondary_structure/__init__.py", line 766, in run if (len(proxies) == 0) : NameError: global name 'proxies' is not defined Am I missing something? Also, is there anything like '-h' on phenix.secondary_structure_restraints so that I can figure out the different options? Thanks, Bradley

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differences between command line and GUI?
by Kendall Nettles 28 Mar '11

28 Mar '11

Dear PHENIX developers, I ran a job through the GUI, and then what I thought was the same job on our cluster. The job from the cluster has Rfree that is 0.7% higher. I'm totally at a loss to figure out what is causing this. It is the same version of PHENIX (1.7-650). I then took the .eff file from the GUI job and used that as the params file for the command line job but still get the big difference in R free. Any suggestions? Best regards, Kendall Nettles

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r_free_flags.export_for_ccp4 option of iotbx.reflection_file_editor
by Keitaro Yamashita 25 Mar '11

25 Mar '11

Dear PHENIX developers, I'm using phenix-1.7-650 (current latest). I noticed that r_free_flags.export_for_ccp4 option of iotbx.reflection_file_editor, which convert flag convention to ccp4 style, does always assign 1..19 to working set at random. In CCP4 style, I think working set flag numbers should be 1 .. (1 / fraction - 1). Otherwise, I'm afraid it might have a bad influence on further processing e.g. flag value completion using ccp4 program. I look forward to your response, Keitaro

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modified nucleotide not linked
by tuske＠cabm.rutgers.edu 25 Mar '11

25 Mar '11

Hello all, I am refining three protein-DNA complexes each with a different modified nucleotide-monophosphate residue at the 3'-terminus of its DNA strand. Two of these worked fine after sending the pdb file through ready-set. With the third structure the modified nucleoside-monophosphate residue is not recognized as linked to the previous nucleotide-monophospahe--no phosphodiester bond formation. The only difference between the two that "worked" and the one that didn't is the nature of the deoxyribose sugar modification. The first two have substituents at the 4'-carbon of the deoxyribose sugar, the third has the 4'-oxygen of the deoxyribose sugar substituted with a -CH2- making it a cylcopentyl pseudo-sugar. The bond lengths and angles are reasonable in the starting model, I had no problem doing the initial refinement in CNS after defining topology and parameter files. The output for this in the log file is: Chain: "P" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 439 Unusual residues: {'CAR': 1} Classifications: {'undetermined': 1, 'DNA': 20} Modifications used: {'5*END': 1} Link IDs: {None: 1, 'rna3p': 19} Not linked: pdbres="CYT P 821 " segid="P " pdbres="CAR P 822 " segid="P " Thanks, Steve

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free R test or work set flag value
by Bryan Lepore 25 Mar '11

25 Mar '11

[ dev-705 ] i see: Test (R-free flags) flag value: 1 is the work set the negation? -Bryan

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Postdoctoral position in Grenoble, France - Living deep
by Eric Girard 25 Mar '11

25 Mar '11

*Living deep: Structural basis of piezophilic adaptation* ELMA group. Institut de Biologie Structurale J.-P. Ebel -- Grenoble -- France http://www.ibs.fr/groupes/groupe-extremophiles-et-grands/ We are recruiting a post-doctoral scientist interested in life adaptation to extreme conditions. The position is for 2 years and is funded by the french national agency for research (ANR) A high-pressure environment characterizes our planet. For more than 60 % of the biosphere pressure is greater than 100 bars and it can reach 1000 bars in the deepest sea trenches, like the Marianna's trench. However, in these extreme conditions, a vast biodiversity of adapted micro-organisms (piezophiles) can be encountered. So far, the molecular mechanisms that facilitate proteins function under high pressure remain obscurs. Beside interests to understand fundamental protein folding processes and life evolution, this information is essential to develop biotechnological application from deep sea enzymes. This work will be performed in the framework of a collaborative network including ENS Lyon and IFREMER-UBO in Brest in which a new archaeon from the Pyroccoccus phylum was recently discovered and was called Pyrococcus yayanosii CH1. This microbe is the first obligate piezophile as it is only able to grow under pressure (optimal growth: 98°C and 520 bars). The project is based on the study of two protein families, for which the biochemistry is well handled by the team: large peptidases complexes and lactate/malate dehydrogenase (LDH/MalDH). These proteins play key roles in metabolic adaptation to deep sea ecosystem and allow combining structural approaches (protein crystallography, small-angle scattering...) and biochemical approaches (oligomer stability, enzymatic activity measurements...). The candidate will study the molecular effects of high pressure/temperature by comparing the structural and functional properties of different proteases and LDH/MalDH from Thermococcus and Pyrococcus phylums (including Pyrococcus yayanossi CH1) isolated at various water depths. The ELMA team possesses a fully-fledged wet laboratory for all biochemical steps and the project will benefit from privileged access to large facilities (synchrotron and neutron sources) as well as from latest developments in high-pressure biophysics: high-pressure protein crystallography, for which the ELMA team is a world leader, small-angle x-ray scattering under high-pressure, UV-Visible spectrophotometer and fluorimeter both equipped with a high-pressure vessel. The candidate should have a background in biochemistry with a strong interest in structural approaches or a physico-chemistry background with a strong interest for biophysics. Candidatures, including CV, intention letter and the names and contact information of referees, as well as informal inquiries should be sent to Eric Girard (eric.girard at ibs.fr) and Bruno Franzetti (bruno.franzetti at ibs.fr). Relevant publications from the team: Coquelle et al (2007) Activity, stability and structural studies of lactate dehydrogenases adapted to extreme thermal environments. J Mol Biol 374: 547-562. Dura et al (2009) The structural and biochemical characterizations of a novel TET peptidase complex from Pyrococcus horikoshii reveal an integrated peptide degradation system in hyperthermophilic Archaea. Mol Microbiol 72: 26-40. Girard et al. (2011). Structure-function perturbation and dissociation of tetrameric urate oxidase by high-hydrostatic pressure. Biophys J 98: 2365-2373. -- *************************************************************** Eric Girard Extremophiles and Large Macromolecular Assemblies (ELMA) group Institut de Biologie Structurale J.-P. Ebel UMR 5075 CEA-CNRS-UJF-PSB 41, Rue Jules Horowitz 38027 Grenoble Cedex 1, France Web site:http://www.ibs.fr/ ***************************************************************

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fwd: Reminder: Fourth annual CCP4 summer school in USA, at APS, June 7-15
by Nathaniel Echols 24 Mar '11

24 Mar '11

---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> Date: Thu, 24 Mar 2011 16:35:22 -0500 Subject: Reminder: Fourth annual CCP4 summer school in USA, at APS, June 7-15 Dear Colleagues, This is a reminder that the deadline for applications for the 4th annual CCP4 summer school “From data collection to structure refinement and beyond” is April 8. The school will take place June 7-15, 2011 at the Advanced Photon Source (APS) near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (the program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2011/ The school will include data collection, processing, structure solution, model building, refinement, validation, automation of many steps etc. Participants are encouraged to bring their own crystals, raw data or processed data for hands-on problem solving under the guidance of software developers and other experts. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences 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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local B-factors
by Priit Eek 24 Mar '11

24 Mar '11

Hi, Talking about B-factors... Being a novice crystallographer I came to a problem: what's the best tool to calculate the average B-factor of a specified region (a domain) in the model, to describe the mobility of chains (or disorder in the crystal) in that region? Regards, Priit

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Multiprocessors/parallel runs keywords
by Jendrek 24 Mar '11

24 Mar '11

Hi, I'm trying to get a grip on what seems to be a multitude of options for running Phenix in multiprocessor/parallel mode. Some of the options/keywords are obvious and easy to find in documentation but other elude me and the posts on the phenixbb make the whole issue even more complicated. So, here is my humble request: Dear Phenix Developers could you please prepare a short summary containing the info concerning running Phenix in multiprocessor/parallel environment for both stable and self compiled developer versions? Even a table with required keywords per program would be a great help... Best regards, Andrzej Lyskowski -- Dr. Andrzej Lyskowski (andrzej[.]lyskowski[(a)]acib[.]at) ACIB Austrian Centre of Industrial Biotechnology GmbH Petersgasse 14, A-8010 Graz, Austria http://acib.at/ c/o IMB Institute of Molecular Biosciences, University of Graz Humboldtstraße 50,III/194, A-8010 Graz, Austria http://strubi.uni-graz.at/ +43 316 380 1993 tel +43 316 380 9897 fax

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