- phenixbb - phenix-online.org

--unused_ok, .def, documentation,...
by Bryan W. Lepore 13 May '09

13 May '09

[ phenix v1.4 rel. tag 3 cctbx tag: 2008_12_07_1353 ] using an old .def w/ "latest devel. rel" phenix (but not nightly) i used --unused_ok b/c it looks like that's what its for. i am expecting an "updated" .def to write after the job - yes?... if so, it reads slightly differently than the documentation.. hard to give an example... things look ok in general, but ought i to have a new .def? -bryan p.s: does phenix write version/release info in the .def (i can't find it)?

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Simulated annealing
by Esmael Haddadian 13 May '09

13 May '09

Hi, I have tried to only refine the sidechains in my model using the simulated annealing with commands strategy=individual_sites sites.individual = "sidechain" However after the refinement the backbone was also moved; any suggestions as how to only allow sidechain movements during the refinement? Thanks, Esmael

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Carbohydrate refinement
by Katya Heldwein 12 May '09

12 May '09

Hi, I have several N-linked sugars in my structure. Some are modeled as single NAGs and others, as NAG-NAG chains. How do I specify Asn-NAG and NAG-NAG linkages for phenix refinement? Currently, when I try to refine the model, NAGs move away from Asn and from each other. Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University School of Medicine 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

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a problem with phenix installation
by Tatyana Sysoeva 11 May '09

11 May '09

Hello, I'm new to Phenix as well as I'm not familiar with Linux OSs. I have Windows Vista OS machine (intel, 32 bit) with VM Player on it. on VM Player I run Fedora 7. I downloaded Phenix 1.4 installation package for Intel-Linux-2.6, ran install. It took more then 10 min, stalled on some lines. Then I run usr/local/phenix-1.4-3/phenix-env.sh. No error messages so far. After I'm done with first two steps and try to start phenix - it says that "command not found". Should I change some path variables, how can I test the installation itself? what should I check first? I guess it might be a very basic or silly question, but I would be very grateful if anybody can help me with this and point out what I have to do to start my work with Phenix. Thank you, Tanya

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tls refinement
by sbiswas2＠ncsu.edu 11 May '09

11 May '09

Hi all, I started doing TLS refinement with one of my structures and got the following: Start R-work = 0.3817, R-free = 0.3923 (no bulk solvent and anisotropic scale) Final R-work = 0.3788, R-free = 0.3885 (no bulk solvent and anisotropic scale) Start R-work = 0.2094, R-free = 0.2381 Final R-work = 0.2058, R-free = 0.2358 my question now is why is the R value high without the anisotropic scale? Second question is: can I refine alternate conformations using the command line or is it already there in the default parameters? Thanks, Shya NC State University

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Phaser, Phenix and Em models
by Gino Cingolani 11 May '09

11 May '09

Hi Randy, what about implementing the use of EM-models (e.g. structure factors from EM model) in Phenix to carry out MR and/or MR-SAD? There's a growing number of macromolecular complexes that have been imaged at medium/low res by EM, which could be of great help to phase at low res or located anomalous scatterers in phased maps. And the EM database keeps growing! At this moment, it is certainly possible to use EM models in Phaser, but the Phenix pipeline could add much more to that. For instance, Phenix would allow for better phase extension of low res EM phases to higher res by ncs-averaging or multi-crystal averaging (in Resolve). Or Phenix could help combining low res EM phases with other phase sources such as SeMet sites, poorly occupied heavy atom sites, etc (MR-SAD). Or Phenix could rigid body refine (at low resolution) pseudo-atomic models obtained by filling in EM-models with dummy atoms. This would help defining averaging masks and so on. What do you think? Thanks in advance, Gino *********************************************************** Gino Cingolani, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology SUNY Upstate Medical University 750 E. Adams Street, Syracuse, NY, 13210 Tel. (315) 464 8744 Fax. (315) 464 8750 Email: cingolag(a)upstate.edu *********************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

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Re: [phenixbb] Phaser, Phenix and Em models
by Gino Cingolani 11 May '09

11 May '09

Hi Randy, thanks for getting back to my email. Yes, I do think it would be very helpful to switch to using density instead of coordinates both for MR and MR-SAD. The interface between cryo-EM and X-ray is growing so fast that in many cases EM densities could be used for initial phasing by Fourier difference, or even ab initio, provided sufficient ncs is available. In our specific case we have at least two macromolecular complexes (1.1-2.2MDa) with >400SeMet, resolutions in the mid 3A with extreme unisomorphism and 10-15A EM densities. SAD/MAD phasing is unrealistic, MIR methods can't work when all crystals are inherently unisomorphic .... MR/MR-SAD could be an alternative. Thanks again! Gino Hi, As it happens, we've been working very hard over the last few months first to make all commands in Phaser available from Python (done) and second to make all options available from the new Phenix GUI (getting close). ("We" in this context mostly means Airlie at our end and Nat at the Berkeley end.) So it should become easy to switch to using density instead of coordinates for your models without switching to the command-line mode of running Phaser. We're also very interested in optimizing the way that we use density from EM, which is something we haven't spent enough time playing with yet. It's not yet possible to use density for a model in the MR-SAD mode--that's been on the wish list and shouldn't be too hard. Do you need that feature right now? I really like your other ideas, so we'll have to talk to Tom about adapting the AutoMR wizard so that it doesn't require a coordinate file. As you say, this will be a real growth area! All the best, Randy On 8 May 2009, at 15:39, Gino Cingolani wrote: > Hi Randy, > > what about implementing the use of EM-models (e.g. structure factors > from EM model) in Phenix to carry out MR and/or MR-SAD? > There's a growing number of macromolecular complexes that have been > imaged > at medium/low res by EM, which could be of great help to > phase at low res or located anomalous scatterers in phased maps. > And the EM database keeps growing! > > At this moment, it is certainly possible to use EM models in Phaser, > but the Phenix pipeline could add much more to that. For instance, > Phenix would allow for better phase extension of low res EM phases > to higher > res by ncs-averaging or multi-crystal averaging (in Resolve). > Or Phenix could help combining low res EM phases with other phase > sources such as SeMet sites, poorly occupied heavy atom sites, etc > (MR-SAD). > Or Phenix could rigid body refine (at low resolution) pseudo-atomic > models > obtained by filling in EM-models with dummy atoms. > This would help defining averaging masks and so on. > What do you think? > > Thanks in advance, > > Gino > > > *********************************************************** > Gino Cingolani, Ph.D. > Assistant Professor > Dept. of Biochemistry and Molecular Biology > SUNY Upstate Medical University > 750 E. Adams Street, Syracuse, NY, 13210 > Tel. (315) 464 8744 > Fax. (315) 464 8750 > Email: cingolag(a)upstate.edu > *********************************************************** > "Nati non foste per viver come bruti, ma per seguir virtute e > conoscenza" > ("You were not born to live like brutes, but to follow virtue and > knowledge") > Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.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 _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb *********************************************************** Gino Cingolani, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology SUNY Upstate Medical University 750 E. Adams Street, Syracuse, NY, 13210 Tel. (315) 464 8744 Fax. (315) 464 8750 Email: cingolag(a)upstate.edu *********************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

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AutoMr
by Zhongli Cui 11 May '09

11 May '09

Dear all, I am using phenix automr to solve my structure. I have 2 search models with identiy of 44% and 31% respectively aligned by ClustalW. I used thiese two pdbs as search models directly in phenix, it gave a llg of about -60 and Tfz of 7. The refined structure fit the map quite well. But I wonder if the solution is OK for the negative LLG. So what should I do next? How should I prepare the search model? Shall I edit the seach models such as remove some loops or surface side chains? If I the a search model prepared by Chainsaw was used, then what is identity I have to tell phenix? Another question, I built 2 models of the same protein and of the same x-ray diffraction data with phaser in CCP4 and Phenix. In my mind, these models should be the same. But in fact they differ from each other significantly in orientation. Is there something wrong with my calculation? ---------------- Cui Zhongli Ph.D Dept. of Microbiology College of Life Sciences Nanjing Agricultural University 1 Weigang, Nanjing, 210095 Jiangsu Province P.R. China. Mail: czl(a)njau.edu.cn Tel: 86-25-84396753 Mob: (0)13951080529

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If HL coefficients are in the .mtz phenix.refine is ignoring my refinement.target= ml specification?
by Francis E Reyes 08 May '09

08 May '09

Hi all (again) It seems that despite me specifying refinement.main.target=ml in my def file, phenix.refine seems to want to keep refining against HL coefficients. It seems overtly out of the way to remove the HL coefficients definition (both the label and file) from the def file as well. Am I doing something wrong then (i.e. does it keep going back to refining experimental phases for some valid reason?) Over 80% of the ASU is built with R/Rfree in high 20's for 1.7 A data. Cheers FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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changes to phenix autosol?
by Francis E Reyes 08 May '09

08 May '09

Hi all It seems that AutoSol now does some initial building when before (at least 1.3-final) it just output a phaser_x.mtz and resolve_x.mtz which would go onto phenix.autobuild after_autosol . What's this new initial building? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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Refining atoms on special positions
by Oliver Clarke 08 May '09

08 May '09

Hi, I'm running phenix.refine v1.4-3, and I'm refining a 3.3A structure that has potassium ions present on a crystallographic fourfold axis. I believe (based on previous refinement in REFMAC5.5), that these ions are at full occupancy, so I set the occupancy of each ion to 1. Despite this, there is still a lot (several 7-10sigma peaks in the Fo- Fc) of unexplained positive density, the potassium ions do not converge to their previously refined positions, and their B-factors refine upwards to values several times higher than the surrounding protein. When the same structure is refined in refmac (with ion occupancy set to 0.25), there is little to no unexplained density and the R/Rfree are substantially lower (21.9/25.9 as against 24.5/31) Does anyone have any ideas/suggestions as to what might be going on? Cheers, Oliver

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torsion_angles
by Imre Toeroe 08 May '09

08 May '09

Dear phenixers, I have seen a new strategy option, *torsion_angles* in the def files produced by recent (1.4-5x) phenix.refine. Is it active? How can one use it? Thanks, Imre

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Refining f'/f"?
by Leigh Allen 07 May '09

07 May '09

Hello, I'm new to the world of x-ray crystallography. I just solved my first SAD structure and I'm on to the refinement stage. The difference map generated by phenix.refine has really big positive peaks all around my MET residues. If I switch the atoms to MSE, then I get large negative peaks. Firstly, I'm not sure if I'm supposed to represent these residues as MET or MSE because it's a "native," high resolution (1.85) dataset, but it the protein had MSE residues. When scaling this data, I did not keep F(+) and F(-) separate. The protein's phases were generated using SAD data to 2.7A, which using SHARP led to a remarkably interpretable map that allowed me to build in the protein by hand. My second question is, how should I handle the issue with large + MET/large - MSE peaks? Do I need to rescale my data to treat it as anomalous data or is there something I can do within Phenix to fix my problem. I tried the phenix.refine GUI and set it up to refine f' and f", but it appears that nothing really changed. Thanks! Leigh Allen ******* Ph.D Candidate McCafferty Lab Department of Chemistry Duke University

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phenix.refine Ile peptide bond breaks
by SIPPEL,KATHERINE H 07 May '09

07 May '09

Hi all, I've got a 2.1 angstrom structure that I am refining. The space group is P212121. The structure is a dimer which I am refining without NCS restraints. Each monomer has 333 residues and one ligand, there are 33 Ile residues in each monomer. The first couple of rounds of refinement I had no problems, but during the third round phenix started breaking the main chain at the peptide bond and the side chain between CA and CB on some of the Ile residues. Specifically there are two breaks in chain A and four breaks in chain B, with two additional residues in chain B breaking only the CA-CB bond. Only one of the breaks is between the same residue in both chains. I'll be boring and run through my refinement process. This is the first time I've used phenix for anything but AutoSol and it is very likely that I have messed something up. Feel free to correct anything else I've done wrong along the way. Round 1, I rigid body refined chain A and B independently, performed simulated annealing, and refined individual coordinates. In COOT I manually refined and removed some bad loops. A few of the Ile were deleted but none of the problem ones Round 2, I refined individual_sites and individual_adp and turned off simulated annealing. In COOT I rebuilt some of the loops and fitted the ligand into the density. I generated a .cif file in eLBOW. Round 3, I refined the same as round 2 except that I included the .cif file. This is when I got the peptide bond breaks for Ile residues. I figured it was a fluke, fixed the breaks in COOT and rebuilt a few more residues in the loops. I ran another round of refinement and the same breaks showed up in the pdb file. I double checked the .geo file to see if Real Space Refine had made the bond distances were too long, but all the input distances were within one or two hundredths of an angstrom from ideal. I considered it was maybe the ADP refinement as I was borderline pushing the number of parameters I was refining given the number of reflections I had. I turned off the individual_adp refinement and reran refine_003. No luck. I tried increasing the weight of the geometry restraints over the observed data. I did this by increasing target_weights.wxc_scale = 1.5. (I suspect that I got this wrong. As I understood the wxc_scale is the ratio of the geometry restraints to the observed data. Feel free to point and laugh as long as you also provide an explanation as to what this parameter really means and how I should have done it,please.) Still no luck. For future information none of the problem isoleucines were located near the ligand or near any of the loops I was rebuilding. I think that's everything. Any help would be appreciated, Thanks, Kat -- SIPPEL,KATHERINE H Ph. D. candidate McKenna Lab Department of Biochemistry and Molecular Biology College of Medicine University of Florida

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difference density maps
by rpai＠berkeley.edu 06 May '09

06 May '09

Hi, I have a question on difference density maps. We are soaking in a substrate into my enzyme and am trying to see if it is in there by looking at difference density maps. We looked at an fobs-(fobs-fcalc) map and see density and 5 sigma at each catalytic active site in roughly the same place, its not great, but it seems like there is something there. so then, I thought I would confirm this by an fobs-fobs map. But I just used the phenix fobs-fobs difference electron density map and I dont see anything there. So I am curious as to an explanation of the difference. Any ideas? Raj

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SA-omit map
by James Fraser 05 May '09

05 May '09

Is there anyway to get phenix.autobuild to NOT delete multiple conformers when doing a SA-omit map? Thanks, jf -- James Fraser jamesfraser(a)berkeley.edu Alber Lab 356 Stanley Hall, QB3 UC Berkeley Berkeley, CA 94720 http://ucxray.berkeley.edu/~jfraser/

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(no subject)
by Leigh Allen 04 May '09

04 May '09

A Python error was detected. This is almost certainly a bug; please send an email containing this message to phenixbb(a)phenix-online.org so we can fix it. Thanks! AttributeError : 'ResultsNotebook' object has no attribute 'file_base' Traceback: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI2/MainWindow.py", line 257, in launch_coot (file_name, file_prefix) = self.pick_model() File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Refine.py", line 386, in pick_model file_base = result_page.file_base AttributeError: 'ResultsNotebook' object has no attribute 'file_base'

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Missing plotting libraries
by Leigh Allen 04 May '09

04 May '09

How do I fix this? You appear to be missing one or more libraries required by the plotting module; plots will be disabled for now. The original error is shown below. liblapack.so.3: cannot open shared object file: No such file or directory You appear to be missing one or more libraries required by the plotting module; plots will be disabled for now. The original error is shown below. liblapack.so.3: cannot open shared object file: No such file or directory Plot library disabled: wxGUI2.Plot disabled. Graphing will be turned off. You appear to be missing one or more libraries required by the plotting module; plots will be disabled for now. The original error is shown below. liblapack.so.3: cannot open shared object file: No such file or directory You appear to be missing one or more libraries required by the plotting module; plots will be disabled for now. The original error is shown below. liblapack.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/usr/local/phenix-1.4-55/phenix/phenix/command_line/refine_gui.py", line 16, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.4-55/phenix/phenix/command_line/refine_gui.py", line 9, in run from wxGUI2.Programs import Refine File "/usr/local/phenix-1.4-55/phenix/wxGUI2/Programs/Refine.py", line 13, in <module> from wxGUI2.Programs import RefineNotebook File "/usr/local/phenix-1.4-55/phenix/wxGUI2/Programs/RefineNotebook.py", line 802, in <module> class ResolutionBinStatsPlot (Plot.Loggraph) : AttributeError: 'NoneType' object has no attribute 'Loggraph'

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Switching off symmetry related van der waals in phenix.refine
by Chandrika Deshpande 01 May '09

01 May '09

Hello everyone, I am using Phenix.refine to refine one of my protein structures. My protein crystallised in the spacegroup P6522 with one protein molecule in the asymmetric unit. I have a PEG molecule from the crystallization condition which crosses a two-fold crystallographic symmetry axis. PEG is symmetric hence this does not violate the crystal symmetry. However, this situation causes a problem which I need to solve : How can I refine this structure to include the PEG molecule? Is there a way to remove van der Waals repulsion between one half occupancy PEG and its crystallographic symmetry mate ? Is there a way to switch off symmetry related van der waals terms from the penalty function in phenix.refine ? I have already tried refining by changing the occupancy of PEG to 0.5 but this does not work as after running refinement the PEG molecule is pushed out of the electron density map. Thanks, Chandrika

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Geometry analysis
by Ulrich Baumann 29 Apr '09

29 Apr '09

Hi, I am just wondering whether there is a tool/feature in Phenix that (i) prints out all bonds/angles deviating by some specified number of standard deviations, and (ii) reads a user-defined .cif file for ligands as well so that this ligand appears in (i) as well. Phenix.pdbtools prints a bond histogram and I did not manage to include an external .cif file. Most likely this is easy to do and I haven't found it in the manual yet. Thanks in advance, Ulrich

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fobs-fobs difference electron density maps
by chandra bose 29 Apr '09

29 Apr '09

Hi, I was wondering how to make fobs-fobs difference electron density maps with phenix using data sets from two crystals. I know cns has a script for this... thanks Charlie

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Re: [phenixbb] Exploded ligands and phenix...
by Ralf W. Grosse-Kunstleve 28 Apr '09

28 Apr '09

Hi Ruben, > The cryst1 card of the pdb is the next: > CRYST1 98.500 104.050 415.200 90.00 90.00 90.00 P 21 21 21 I tried phenix.pdbtools --geometry-regularization again after adding this CRYST1 card. The result looks good, i.e. symmetry interactions don't seem to be the problem. > For non-bound interactions the distance is sometimes > less than the VDW-radius. Could this be the problem? No, I don't think so. Your histogram of nonbonded interaction distances looks reasonable. > The log file can be downloaded here: > files.me.com/ruben.vandermeeren/9tuifv Clearly, the .cif file is read, otherwise phenix.refine would stop very early on. Sorry, I still don't know what's going wrong. Could you send me the phenix.refine inputs for debugging (to me directly, not to phenixbb)? Ralf

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Exploded ligands and phenix...
by Ruben Van der Meeren 28 Apr '09

28 Apr '09

Hi, I'm using phenix for the refinement of my protein (phenix.refine). But there is a problem... My protein contains a ligand. For this ligand I use the optimal coordinates wich I downloaded from the HIC-Up server. Then, as coot and phenix need a cif file, I generate a cif file using the PRODRG Server and select (copy-paste) the Refmac5 output --> *.cif . Below you can see the content of this cif file and also the pdb file. Coot can use this cif file. But when I refine the protein (e.g. even only individual sites) the ligand "explodes". In coot you then see only single atoms and no bonds. To illustrate this you can see a pictures on this website: http://gallery.me.com/ruben.vandermeeren#100216 --> "exploded" First I thought that phenix could not find the cif file, but the correct path (via monomers) is given in the parameter file and I also used the command line to import the cif file, but still the ligand "explodes". I use the latest version of phenix for mac (phenix-1.4-3). But more important: I also tried refmac (from ccp4) to refined my protein with it and here there is "no explosion". So refmac does something that phenix doens't: it can refine my protein with the ligand. You can see the nice picture on this website: http://gallery.me.com/ruben.vandermeeren#100216 --> "as it should be". So my question is on how to resolve the issue using phenix.refine. Is phenix somehow unable to read the contents of the cif file? Best regards, Ruben -------------------------------------------------------------------------------------------------------------------------------------------------------- PDB COMPND TRE TREHALOSE; ALPHA-D-GLUCOPYRANOSYL-ALPHA-D-GLUCOPYRANOSIDE REMARK TRE Part of HIC-Up: http://xray.bmc.uu.se/hicup REMARK TRE Extracted from PDB file pdb1j1m.ent REMARK TRE Formula C12 H22 O11 REMARK TRE Nr of non-hydrogen atoms 23 REMARK TRE Eigen-values covariance X/Y/Z 187.8 54.6 26.5 REMARK TRE Residue type TRE REMARK TRE Residue name 7347 REMARK TRE Original residue name (for O) $304 REMARK TRE RESOLUTION. 1.50 ANGSTROMS. REMARK TRE occurs in 21 other PDB entries REMARK TRE Also in <1.5A : 2BHY 2BY2 2BY3 2Z3G REMARK TRE Resolution (A) : 1.50 1.50 1.50 1.50 REMARK TRE Also in 1.5-2.0A : 2BY0 2BY1 2BXY 2BXZ 1EU8 1F0P 2EBF 2CY6 2E4P REMARK TRE Resolution (A) : 1.55 1.55 1.75 1.75 1.90 1.90 1.90 2.00 2.00 REMARK TRE Also in 2.0-2.5A : 2DXY 2FPD 1NI6 2B1Q 1V6A 2E50 2EBH REMARK TRE Resolution (A) : 2.03 2.05 2.10 2.20 2.30 2.30 2.40 REMARK TRE Also in 2.5-3.0A : 1TEX REMARK TRE Resolution (A) : 2.60 REMARK TRE HETATM 1 C1 TRE 7347 1.108 0.876 0.900 1.00 20.00 HETATM 2 C2 TRE 7347 1.959 1.953 0.170 1.00 20.00 HETATM 3 C3 TRE 7347 2.717 1.276 -1.006 1.00 20.00 HETATM 4 C4 TRE 7347 3.662 0.237 -0.355 1.00 20.00 HETATM 5 C5 TRE 7347 2.806 -0.843 0.385 1.00 20.00 HETATM 6 C6 TRE 7347 3.596 -1.917 1.069 1.00 20.00 HETATM 7 O1 TRE 7347 0.133 0.432 0.010 1.00 20.00 HETATM 8 O2 TRE 7347 1.086 2.923 -0.297 1.00 20.00 HETATM 9 O3 TRE 7347 3.472 2.234 -1.665 1.00 20.00 HETATM 10 O4 TRE 7347 4.408 -0.441 -1.302 1.00 20.00 HETATM 11 O5 TRE 7347 1.964 -0.233 1.404 1.00 20.00 HETATM 12 O6 TRE 7347 2.687 -2.806 1.676 1.00 20.00 HETATM 13 C1P TRE 7347 -0.814 -0.557 0.430 1.00 20.00 HETATM 14 C2P TRE 7347 -1.601 -1.752 -0.126 1.00 20.00 HETATM 15 C3P TRE 7347 -2.572 -1.142 -1.231 1.00 20.00 HETATM 16 C4P TRE 7347 -3.557 -0.224 -0.472 1.00 20.00 HETATM 17 C5P TRE 7347 -2.743 0.960 0.225 1.00 20.00 HETATM 18 C6P TRE 7347 -3.666 1.891 1.015 1.00 20.00 HETATM 19 O2P TRE 7347 -0.693 -2.574 -0.755 1.00 20.00 HETATM 20 O3P TRE 7347 -3.323 -2.155 -1.812 1.00 20.00 HETATM 21 O4P TRE 7347 -4.483 0.363 -1.367 1.00 20.00 HETATM 22 O5P TRE 7347 -1.775 0.343 1.115 1.00 20.00 HETATM 23 O6P TRE 7347 -4.371 1.155 1.989 1.00 20.00 REMARK TRE ENDHET -------------------------------------------------------------------------------------------------------------------------------------------------------- CIF # WARNING: REFMAC5 uses columns 77-78 of PDB ATOM records to # establish equivalence between model and topology. If # you use O or other programmes that produce defective # PDB files you must restore these columns, otherwise # REFMAC5 will not recognise this topology. # # # This file was generated by PRODRG version 071121.0636 # PRODRG written/copyrighted by Daan van Aalten # and Alexander Schuettelkopf # # Questions/comments to dava(a)davapc1.bioch.dundee.ac.uk # # When using this software in a publication, cite: # A. W. Schuettelkopf and D. M. F. van Aalten (2004). # PRODRG - a tool for high-throughput crystallography # of protein-ligand complexes. # Acta Crystallogr. D60, 1355--1363. # # global_ _lib_name prodrg_lib _lib_version 71121 _lib_update ? # # --------------- # data_comp_list # loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level TRE TRE 'TRE ' non-polymer 45 23 . # # --------------- # data_comp_TRE # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge TRE O2 O OH1 -0.115 TRE HAA H HOH1 0.028 TRE C2 C CH1 0.074 TRE 1H2 H HCH1 0.000 TRE C3 C CH1 0.074 TRE 1H3 H HCH1 0.000 TRE O3 O OH1 -0.115 TRE HAB H HOH1 0.028 TRE C4 C CH1 0.074 TRE 1H4 H HCH1 0.000 TRE O4 O OH1 -0.115 TRE HAC H HOH1 0.028 TRE C5 C CH1 0.126 TRE 1H5 H HCH1 0.000 TRE C6 C CH2 0.037 TRE 1H6 H HCH2 0.000 TRE 2H6 H HCH2 0.000 TRE O6 O OH1 -0.115 TRE HAD H HOH1 0.028 TRE O5 O O2 -0.109 TRE C1 C CH1 0.126 TRE 1H1 H HCH1 0.000 TRE O1 O O2 -0.109 TRE C1P C CH1 0.126 TRE 1H1P H HCH1 0.000 TRE O5P O O2 -0.109 TRE C5P C CH1 0.126 TRE 1H5P H HCH1 0.000 TRE C6P C CH2 0.037 TRE 1H6P H HCH2 0.000 TRE 2H6P H HCH2 0.000 TRE O6P O OH1 -0.115 TRE HAH H HOH1 0.029 TRE C4P C CH1 0.074 TRE 1H4P H HCH1 0.000 TRE O4P O OH1 -0.115 TRE HAG H HOH1 0.028 TRE C3P C CH1 0.074 TRE 1H3P H HCH1 0.000 TRE O3P O OH1 -0.115 TRE HAF H HOH1 0.028 TRE C2P C CH1 0.074 TRE 1H2P H HCH1 0.000 TRE O2P O OH1 -0.115 TRE HAE H HOH1 0.028 loop_ _chem_comp_tree.comp_id _chem_comp_tree.atom_id _chem_comp_tree.atom_back _chem_comp_tree.atom_forward _chem_comp_tree.connect_type TRE O2 n/a C2 START TRE HAA O2 . . TRE C2 O2 C1 . TRE 1H2 C2 . . TRE C3 C2 C4 . TRE 1H3 C3 . . TRE O3 C3 HAB . TRE HAB O3 . . TRE C4 C3 C5 . TRE 1H4 C4 . . TRE O4 C4 HAC . TRE HAC O4 . . TRE C5 C4 O5 . TRE 1H5 C5 . . TRE C6 C5 O6 . TRE 1H6 C6 . . TRE 2H6 C6 . . TRE O6 C6 HAD . TRE HAD O6 . . TRE O5 C5 . . TRE C1 C2 O1 . TRE 1H1 C1 . . TRE O1 C1 C1P . TRE C1P O1 C2P . TRE 1H1P C1P . . TRE O5P C1P C5P . TRE C5P O5P C4P . TRE 1H5P C5P . . TRE C6P C5P O6P . TRE 1H6P C6P . . TRE 2H6P C6P . . TRE O6P C6P HAH . TRE HAH O6P . . TRE C4P C5P C3P . TRE 1H4P C4P . . TRE O4P C4P HAG . TRE HAG O4P . . TRE C3P C4P O3P . TRE 1H3P C3P . . TRE O3P C3P HAF . TRE HAF O3P . . TRE C2P C1P O2P . TRE 1H2P C2P . . TRE O2P C2P HAE . TRE HAE O2P . END TRE O5 C1 . ADD TRE C3P C2P . ADD loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd TRE O2 HAA single 1.000 0.027 TRE O2 C2 single 1.430 0.025 TRE C2 C3 single 1.530 0.025 TRE C2 C1 single 1.530 0.025 TRE C3 O3 single 1.430 0.025 TRE C3 C4 single 1.530 0.025 TRE O3 HAB single 1.000 0.027 TRE C4 O4 single 1.430 0.025 TRE C4 C5 single 1.530 0.025 TRE O4 HAC single 1.000 0.027 TRE C5 C6 single 1.530 0.033 TRE C5 O5 single 1.435 0.033 TRE C6 O6 single 1.430 0.025 TRE O6 HAD single 1.000 0.027 TRE O5 C1 single 1.435 0.033 TRE C1 O1 single 1.435 0.033 TRE O1 C1P single 1.435 0.033 TRE C1P O5P single 1.435 0.033 TRE C1P C2P single 1.530 0.025 TRE O5P C5P single 1.435 0.033 TRE C5P C6P single 1.530 0.033 TRE C5P C4P single 1.530 0.025 TRE C6P O6P single 1.430 0.025 TRE O6P HAH single 1.000 0.027 TRE C4P O4P single 1.430 0.025 TRE C4P C3P single 1.530 0.025 TRE O4P HAG single 1.000 0.027 TRE C3P O3P single 1.430 0.025 TRE C3P C2P single 1.530 0.025 TRE O3P HAF single 1.000 0.027 TRE C2P O2P single 1.430 0.025 TRE O2P HAE single 1.000 0.027 TRE C2 1H2 single 1.000 0.020 TRE C3 1H3 single 1.000 0.020 TRE C4 1H4 single 1.000 0.020 TRE C5 1H5 single 1.000 0.020 TRE C6 1H6 single 1.000 0.020 TRE C6 2H6 single 1.000 0.020 TRE C1 1H1 single 1.000 0.020 TRE C1P 1H1P single 1.000 0.020 TRE C5P 1H5P single 1.000 0.020 TRE C6P 1H6P single 1.000 0.020 TRE C6P 2H6P single 1.000 0.020 TRE C4P 1H4P single 1.000 0.020 TRE C3P 1H3P single 1.000 0.020 TRE C2P 1H2P single 1.000 0.020 loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd TRE HAA O2 C2 109.500 3.158 TRE O2 C2 C3 109.500 2.727 TRE O2 C2 C1 109.500 2.727 TRE C3 C2 C1 111.000 2.727 TRE C2 C3 O3 109.500 2.727 TRE C2 C3 C4 111.000 2.727 TRE O3 C3 C4 109.500 2.727 TRE C3 O3 HAB 109.500 3.158 TRE C3 C4 O4 109.500 2.727 TRE C3 C4 C5 111.000 2.727 TRE O4 C4 C5 109.500 2.727 TRE C4 O4 HAC 109.500 3.158 TRE C4 C5 C6 109.500 5.000 TRE C4 C5 O5 109.500 4.412 TRE C6 C5 O5 109.500 4.412 TRE C5 C6 O6 109.500 2.727 TRE C6 O6 HAD 109.500 3.158 TRE C5 O5 C1 109.500 3.750 TRE C2 C1 O5 109.500 4.412 TRE C2 C1 O1 109.500 4.412 TRE O5 C1 O1 109.500 4.412 TRE C1 O1 C1P 109.500 3.750 TRE O1 C1P O5P 109.500 4.412 TRE O1 C1P C2P 109.500 4.412 TRE O5P C1P C2P 109.500 4.412 TRE C1P O5P C5P 109.500 3.750 TRE O5P C5P C6P 109.500 4.412 TRE O5P C5P C4P 109.500 4.412 TRE C6P C5P C4P 109.500 5.000 TRE C5P C6P O6P 109.500 2.727 TRE C6P O6P HAH 109.500 3.158 TRE C5P C4P O4P 109.500 2.727 TRE C5P C4P C3P 111.000 2.727 TRE O4P C4P C3P 109.500 2.727 TRE C4P O4P HAG 109.500 3.158 TRE C4P C3P O3P 109.500 2.727 TRE C4P C3P C2P 111.000 2.727 TRE O3P C3P C2P 109.500 2.727 TRE C3P O3P HAF 109.500 3.158 TRE C1P C2P C3P 111.000 2.727 TRE C1P C2P O2P 109.500 2.727 TRE C3P C2P O2P 109.500 2.727 TRE C2P O2P HAE 109.500 3.158 TRE O2 C2 1H2 109.500 3.300 TRE C2 C3 1H3 109.500 3.300 TRE C3 C4 1H4 109.500 3.300 TRE C4 C5 1H5 109.500 3.300 TRE C5 C6 1H6 109.500 3.300 TRE C5 C6 2H6 109.500 3.300 TRE C2 C1 1H1 109.500 3.300 TRE O1 C1P 1H1P 109.500 3.300 TRE O5P C5P 1H5P 109.500 3.300 TRE C5P C6P 1H6P 109.500 3.300 TRE C5P C6P 2H6P 109.500 3.300 TRE C5P C4P 1H4P 109.500 3.300 TRE C4P C3P 1H3P 109.500 3.300 TRE C1P C2P 1H2P 109.500 3.300 loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period TRE var_001 C1 C2 O2 HAA 60.000 13.333 3 TRE CONST_001 C4 C3 C2 O2 60.000 0.714 3 TRE CONST_002 O2 C2 C1 O1 60.000 0.714 3 TRE var_002 C2 C3 O3 HAB 60.000 13.333 3 TRE CONST_003 C5 C4 C3 C2 60.000 0.714 3 TRE var_003 C3 C4 O4 HAC 60.000 13.333 3 TRE CONST_004 C3 C4 C5 O5 60.000 0.714 3 TRE var_004 C4 C5 C6 O6 60.000 2.857 3 TRE CONST_005 C4 C5 O5 C1 60.000 1.111 3 TRE var_005 C5 C6 O6 HAD 60.000 13.333 3 TRE CONST_006 O1 C1 O5 C5 60.000 1.111 3 TRE var_006 C2 C1 O1 C1P 60.000 4.444 3 TRE var_007 C2P C1P O1 C1 60.000 4.444 3 TRE CONST_007 O1 C1P O5P C5P 60.000 1.111 3 TRE CONST_008 O1 C1P C2P O2P 60.000 0.714 3 TRE CONST_009 C4P C5P O5P C1P 60.000 1.111 3 TRE var_008 O5P C5P C6P O6P 60.000 2.857 3 TRE CONST_010 O5P C5P C4P C3P 60.000 0.714 3 TRE var_009 C5P C6P O6P HAH 60.000 13.333 3 TRE var_010 C5P C4P O4P HAG 60.000 13.333 3 TRE CONST_011 C2P C3P C4P C5P 60.000 0.714 3 TRE var_011 C4P C3P O3P HAF 60.000 13.333 3 TRE CONST_012 O2P C2P C3P C4P 60.000 0.714 3 TRE var_012 C1P C2P O2P HAE 60.000 13.333 3 loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign TRE chir_001 C2 O2 C3 C1 positiv TRE chir_002 C3 C2 C4 O3 positiv TRE chir_003 C4 C3 O4 C5 positiv TRE chir_004 C5 C4 O5 C6 positiv TRE chir_005 C1 C2 O5 O1 positiv TRE chir_006 C1P O1 C2P O5P positiv TRE chir_007 C5P O5P C6P C4P positiv TRE chir_008 C4P C5P C3P O4P positiv TRE chir_009 C3P C4P O3P C2P positiv TRE chir_010 C2P C1P O2P C3P positiv # # --------------- # ____________________________________________________________________ Ruben Van der Meeren Bachelor in biochemistry and biotechnology Adress: de Pretlaan 26, B9850 Nevele Tel.: +32478/217480 E-Mail: ruben.vandermeeren(a)mac.com; ruben.vandermeeren(a)ugent.be URL: http://web.mac.com/ruben.vandermeeren iChat: ruben.vandermeeren(a)mac.com Skype: ruben_van_der_meeren

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Optimizing mask parameters for twinned data
by Katya Heldwein 27 Apr '09

27 Apr '09

Hi, is it possible to optimize mask parameters for a model refined with a twinning operator? When I try to do so using optimize_mask=true option, I get the error message: AttributeError: 'twin_model_manager' object has no attribute 'optimize_mask_and_update_solvent_and_scale'. Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

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fwd: Resolve on Mac
by Nathaniel Echols 27 Apr '09

27 Apr '09

(Forwarded on behalf of James Naismith - I have no idea why the server rejected this message.) Begin forwarded message: > From: James Naismith <naismith(a)st-andrews.ac.uk> > Date: April 23, 2009 9:24:05 AM PDT > To: phenixbb(a)phenix-online.org > Subject: Resolve on Mac > > > This is not a bug but some feature of the new Mac (or perhaps mine > is broken). > > Tom Terwilliger can run the same job on his older Mac and on Linux. > However, with my new Mac resolve complains that it can't allocate > enough memory. > > Since my machine has 8GB of memory and Tom's has 2 GB, it is > something to do with the esetup either Mac or Phenix. > > I am a newbie on the Mac, I wondered if anyone could help me. (Tom > is also new to Mac and agreed to my posting here). > > best > Jim > > > Hardware Overview: > > Model Name: MacBook Pro > Model Identifier: MacBookPro5,2 > Processor Name: Intel Core 2 Duo > Processor Speed: 2.93 GHz > Number Of Processors: 1 > Total Number Of Cores: 2 > L2 Cache: 6 MB > Memory: 8 GB > Bus Speed: 1.07 GHz > Boot ROM Version: MBP52.008E.B00 > SMC Version: 1.42f4 > Serial Number: W89090Y82QT > Sudden Motion Sensor: > State: Enabled > > > > -- > James H. Naismith FRSE | mailto:[email protected] > Professor of Chemical Biology | mailto:[email protected] > (teaching) > Centre for Biomolecular Sciences|Office: (44) or (0) 1334463792 > The North Haugh |Secretary: (44) or (0) 1334463401 > The University Sciences |Fax: (44) or (0) 1334467229 > Fife KY16 9ST U.K. |http://www.st-and.ac.uk/~strucbio > > The University of St Andrews is a charity registered in Scotland : > No SC013532 > > >

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