- phenixbb - phenix-online.org

creating map file only
by Raja Dey 15 May '09

15 May '09

Dear Friends, I was trying to create map file only as follows: phenix.refine 1205A-p21212.mtz may15_1_001.pdb map.params strategy=none output.prefix=may15_2 , map.params is as follows refinement { electron_density_maps { map { mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT likelihood_weighted = True obs_factor = 2 calc_factor = 1 } map { mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT likelihood_weighted = True obs_factor = 1 calc_factor = 1 } map { mtz_label_amplitudes = 3FO2FCWT mtz_label_phases = PH3FO2FCWT likelihood_weighted = False obs_factor = 3 calc_factor = 2 } grid_resolution_factor = 1/4. region = *selection cell atom_selection = name CA or name N or name C apply_sigma_scaling = False apply_volume_scaling = True } } But, still I am getting only the map_coeffs.mtz file in the output. I am expecting 3 map files in the output. Could you please tell what's wrong I am doing. I want to create only the map file without any refinement. Looking forward to hearing from you... Regards... Raja

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Beamtime proposal deadline for ALS GU time
by Peter Zwart 15 May '09

15 May '09

May 15, 2009 is the deadline for the July-August Rapid Access Proposal cycle. Please note that the ALS will be shut down in September, 2009. The deadline for applications of beamtime on the BCSB beamlines in the ALS is today! Other notable features include: * A high-accuracy microdiffractometer on BL 8.2.1 allows for centering and viewing of very small crystals; * Robot automounters on BL8.2.1 and 8.2.2 are now fully commissioned. * A new large format (315mm active surface area) CCD detector on BL 8.2.1 facilitates data collection on large unit cell crystals. * Beamlines 5.0.1 and 5.0.3 now generate 1.5x1011 photons per second at 0.97 Angstrom. This wavelength is slightly above the Se K edge making them ideal for performing Se SAD experiments. * Beamline 5.0.2 (a tunable beamline) generates a peak flux of 8x1011 photons per second, and the energy range of 5.0.2 has been extended to 17 keV, enabling the routine use of shorter wavelengths and anomalously scattering elements such as bromine. All beamlines of the BCSB (5.0.1, 5.0.2, 5.0.3, 8.2.1 and 8.2.2) can all be operated remotely. Please contact Peter Zwart (sector 5 beamlines) or Corie Ralston (sector 8 beamlines) for more information. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. To find out more, click on: http://www.als.lbl.gov/als/quickguide/independinvest.html Scroll down to "Structural Biology and SAXS." We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize If you'd like to apply for October-November-December beamtime at the Advanced Light Source, please submit a General User proposal by August 15, 2009. If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime. Cheers, Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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March 15, 2009 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 14 May '09

14 May '09

Dear Users, The deadline for July/August 2009 Collaborative Crystallography proposals will be May 15, 2009. ============= Thumbnail Description: Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ============= How To Apply: To submit a proposal, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html Scroll down to "Structural Biology and SAXS" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only ?) * In question 9, please describe a specific research project with a clear end point. In order to request CC time for July/August 2009allocation period, proposals must be submitted by *May 15, 2009*. Please note that the ALS will be shut down in September, 2009. The deadline for CC proposals for the time period October/November/December 2009 will be August 15, 2009. Regards, Banumathi Sankaran

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--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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