- phenixbb - phenix-online.org

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 30 Mar '11

30 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 30 Mar '11

30 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 29 Mar '11

29 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 29 Mar '11

29 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 26 Mar '11

26 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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weird B factor refinement
by Sebastiano Pasqualato 24 Mar '11

24 Mar '11

Hi all, I am refining a structure and have turned on TLS refinement. Since I have done this, I see a weird behavior in some sulphur atom's B factor, and their near atoms. I paste below an example. Has anybody else seen this? Looks like a bug... Thanks a lot in advance, ciao, s ATOM 655 N PHE A 82 66.343 -40.145 -6.536 1.00 25.85 N ANISOU 655 N PHE A 82 3247 3386 3190 162 103 157 N ATOM 656 CA PHE A 82 65.631 -38.890 -6.206 1.00 23.86 C ANISOU 656 CA PHE A 82 2967 3126 2971 192 102 153 C ATOM 657 C PHE A 82 64.134 -39.032 -6.460 1.00 27.82 C ANISOU 657 C PHE A 82 3494 3640 3436 176 116 173 C ATOM 658 O PHE A 82 63.709 -39.388 -7.568 1.00 46.67 O ANISOU 658 O PHE A 82 5852 6065 5815 251 147 222 O ATOM 659 CB PHE A 82 66.174 -37.668 -6.970 1.00 14.67 C ANISOU 659 CB PHE A 82 1831 1971 1772 176 119 175 C ATOM 660 CG PHE A 82 65.501 -36.397 -6.574 1.00 25.83 C ANISOU 660 CG PHE A 82 3217 3375 3223 210 117 169 C ATOM 661 CD1 PHE A 82 64.399 -35.932 -7.285 1.00 19.12 C ANISOU 661 CD1 PHE A 82 2363 2528 2371 221 125 179 C ATOM 662 CD2 PHE A 82 65.919 -35.707 -5.429 1.00 37.72 C ANISOU 662 CD2 PHE A 82 4725 4876 4732 206 117 168 C ATOM 663 CE1 PHE A 82 63.734 -34.784 -6.874 1.00 23.74 C ANISOU 663 CE1 PHE A 82 2979 3122 2919 200 145 205 C ATOM 664 CE2 PHE A 82 65.275 -34.544 -5.018 1.00 34.01 C ANISOU 664 CE2 PHE A 82 4257 4438 4226 262 171 240 C ATOM 665 CZ PHE A 82 64.176 -34.080 -5.744 1.00 33.79 C ANISOU 665 CZ PHE A 82 4254 4389 4196 197 145 203 C ATOM 666 N CYS A 83 63.337 -38.791 -5.425 1.00 35.53 N ANISOU 666 N CYS A 83 4471 4615 4413 176 117 175 N ATOM 667 CA CYS A 83 61.879 -38.960 -5.524 1.00 55.90 C ANISOU 667 CA CYS A 83 7050 7200 6991 181 121 181 C ATOM 668 C CYS A 83 61.332 -37.537 -5.259 1.00 48.88 C ANISOU 668 C CYS A 83 6132 6340 6100 265 163 240 C ATOM 669 O CYS A 83 61.949 -36.777 -4.512 1.00 50.54 O ANISOU 669 O CYS A 83 6344 6544 6313 262 165 239 O ATOM 670 CB CYS A 83 61.343 -40.122 -4.596 1.00 2.87 C ANISOU 670 CB CYS A 83 332 481 275 174 114 172 C ATOM 671 SG CYS A 83 61.739 -41.776 -5.153 1.00212.79 S ANISOU 671 SG CYS A 83 26919 27069 26861 166 105 162 S ATOM 672 N ASP A 84 60.251 -37.131 -5.925 1.00 46.73 N ANISOU 672 N ASP A 84 5887 6042 5827 199 138 202 N ATOM 673 CA ASP A 84 59.894 -35.684 -6.003 1.00 53.97 C ANISOU 673 CA ASP A 84 6774 6990 6743 291 187 268 C ATOM 674 C ASP A 84 59.468 -34.966 -4.713 1.00 54.16 C ANISOU 674 C ASP A 84 6797 6968 6812 239 140 198 C ATOM 675 O ASP A 84 59.898 -33.835 -4.448 1.00 54.40 O ANISOU 675 O ASP A 84 6861 7005 6804 211 158 221 O ATOM 676 CB ASP A 84 58.829 -35.479 -7.062 1.00 52.17 C ANISOU 676 CB ASP A 84 6574 6736 6511 218 157 225 C ATOM 677 CG ASP A 84 59.320 -35.845 -8.416 1.00 59.41 C ANISOU 677 CG ASP A 84 7456 7647 7469 252 143 207 C ATOM 678 OD1 ASP A 84 60.375 -35.284 -8.783 1.00 61.87 O ANISOU 678 OD1 ASP A 84 7770 7956 7782 252 144 207 O ATOM 679 OD2 ASP A 84 58.683 -36.697 -9.087 1.00 57.64 O ANISOU 679 OD2 ASP A 84 7230 7428 7243 253 141 207 O -- 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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B factor statistics
by Yuri 24 Mar '11

24 Mar '11

Hello phenixers, I am putting together a crystallography table for my model, what is the best way to find the average B factors. Are they broken down by main chain, side chain and HOH? thank you -- Yuri Pompeu

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reference model
by Kendall Nettles 24 Mar '11

24 Mar '11

Dear PHENIX developers, I would like to use a reference model in refinement, but the structure has two components with known higher resolution structures. Can I specify two reference models? How? I'm also having trouble with the syntax. With the following params file, the run fails saying that reference model is an unused parameter. Lastly, what does "reference_xray_structure" do? Thanks! Kendall refinement.main { reference_model_restraints = True } refinement.refine { strategy = *individual_sites \ rigid_body \ individual_sites_real_space \ *individual_adp \ group_adp \ tls \ occupancies \ group_anomalous \ none } reference_model { file = 4.pdb }

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Re: [phenixbb] rotamers
by Phoebe Rice 24 Mar '11

24 Mar '11

I'm moderately in favor of the "just let B go through the roof" option. Here's why: Most "user friendly" programs like pymol have an option to color the atoms by B but not by occupancy. Most end-users I interact with know enough to see if coloring by B makes a side chain flaming red, but they'd never think (or know how) to check occupancy. (So if you do set occ to zero, please set B to the max!) And truncating side chains screws up simple electrostatics calculations, which matters if you deal with nucleic acid-binding proteins. 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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pdb editor after autobuild
by Jason 23 Mar '11

23 Mar '11

Hi, I have a pdb file obtained from autobuild. However, some of the sidechains are missing. Is there an easy way to detect which sidechains are missing? The reason I am asking is my pdb file is huge. It takes a lot of effort to go through one reside by one residue. Thanks. -- ====================== Jason Structural Biology Department University of Pittsburgh ======================

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Low rmsd values
by Teemu Haikarainen 23 Mar '11

23 Mar '11

Hi all, I am getting quite low rmsd values for my structure. I am finishing the refinement and I have rmsd of 0.003 Å for bonds and 0.67 for angles, with R/Rfree of 0.148/0.176. The resolution is 2.0 Å. I am refining with riding hydrogens and using the automatic weight optimization. I have also tried to change the weights manually, but the more eye-pleasing rmsd values always result in worse Rfree. Is there any reason to worry about the low rmsd values and should I always use the optimized weights in refinement? I am using the latest version of Phenix. Regards, Teemu -- Teemu Haikarainen (M.Sc.) Turku Centre for Biotechnology Tykistokatu 6 BioCity, Turku FIN-20521, Finland

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Re: [phenixbb] Autobuild parent process aborted--running combine_models in Autobuild
by Thomas C. Terwilliger 23 Mar '11

23 Mar '11

Hi Mark, The answer depends on whether this is a "rebuild_in_place=True" run or not. (I think you are using rebuild_in_place=true, but I'll give both answers): Assuming "rebuild_in_place=True": You can combine models with autobuild, providing all models have exactly the same set of atoms (aside from any solvent) by editing this script (basically you run a dummy autobuild run to create a directory and database entries, then you copy your files there, then you run autobuild and tell it to carry on and do the combine step): #!/bin/csh -f if (-d PDS || -d AutoBuild_run_1_) then echo "Please run in a directory without PDS or AutoBuild_run_1_" exit 1 endif echo "Setting up combine models with a dummy run. NOTE: multiple_models_group_number must be correct" phenix.autobuild fobs.mtz multiple_models=true seq_file=seq.dat combine_only=true multiple_models_group_number=2 multiple_models_number=1>& dummy_autobuild.log echo "Copying files to AutoBuild_run_1_/MULTIPLE_MODELS" mkdir AutoBuild_run_1_/MULTIPLE_MODELS cp coords1.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_1 cp coords2.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_2 cp map_coeffs_1.mtz AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_1 cp map_coeffs_2.mtz AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_2 ls AutoBuild_run_1_/MULTIPLE_MODELS/ echo "Running autobuild to combine files in AutoBuild_run_1_/MULTIPLE_MODELS" phenix.autobuild combine_only=true seq_file=seq.dat carry_on=true run=1 > autobuild_combine.log # END OF COMBINE_MODELS SCRIPT Assuming "rebuild_in_place=False": In this case you can provide autobuild with a list of files with consider_main_chain_list="file1.pdb file2.pdb" , or simply dump all the models into a singe pdb file and use model=all_models.pdb, and run autobuild one more time. Let me know if that doesn't do it! -Tom On Mar 22, 2011, at 3:00 PM, Mark A Saper wrote: I ran AutoBuild from command line and it submitted 5 jobs with qsub. Apparently I aborted the parent process. So I have the 5 jobs running, apparently producing 5 different models (I specified nproc = 5 as suggested in the documentation). Can I rerun AutoBuild and have it combine the 5 models already calculated? Mark _________________________________ Mark A. Saper, Ph.D. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

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Autobuild parent process aborted
by Mark A Saper 22 Mar '11

22 Mar '11

I ran AutoBuild from command line and it submitted 5 jobs with qsub. Apparently I aborted the parent process. So I have the 5 jobs running, apparently producing 5 different models (I specified nproc = 5 as suggested in the documentation). Can I rerun AutoBuild and have it combine the 5 models already calculated? Mark _________________________________ Mark A. Saper, Ph.D. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

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Another question about twinned maps
by Mary Ho 22 Mar '11

22 Mar '11

Pavel- Another related question... Does the option for Fill Missing F(Obs) with F(Calc) work for twinned maps? If I turn it on, I don't get an error but the maps don't seem any different. Just wondering, Thanks, Mary On Mon, Mar 21, 2011 at 11:44 AM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > Hi Mary, > > I'm not sure map sharpening is done in case of twinning (otherwise it is an > option that you can turn on/off either in phenix.refine or in more specific > tool for maps calculation called phenix.maps). I will check this later today > and reply. > > Pavel. > > > > On 3/21/11 8:08 AM, Mary Ho wrote: > >> I'm using phenix-1.7-650. When phenix.refine generates the detwinned maps >> with apply B-factor sharpening on and no value inputed, is the value the >> program uses for sharpening output anywhere? >> >> Thanks, >> >> Mary X. Ho >> Postdoctoral Associate >> Arnold Lab >> Rutgers >> > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

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