May 2009 - phenixbb - phenix-online.org

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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