- phenixbb - phenix-online.org

IndexError
by Huiying Li 19 Mar '09

19 Mar '09

I was running phenix refinement using the following command: phenix.refine data.mtz model.pdb \ strategy=individual_sites+tls+individual_adp \ my_lib.cif tls.params the run crashed with the error: ...... ...... File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/monomer_library/pdb_interpretation.py", line 970, in get_lib_link atom_dicts[angle.atom_3_comp_id].get(angle.atom_id_3, None)] IndexError: list index out of range Is the index error refering to some problem in the reflection file (mtz)? Thanks for any suggestions. Huiying _____ Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: hli(a)uci.edu

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Can Phenix do MR with medium/low res EM models?
by Gino Cingolani 19 Mar '09

19 Mar '09

Hi Phenix community, I was wondering if Phenix can handle MR starting from medium/low res EM models. I have a very large oligomeric protein (2.4MDa) with lots of NCS and >450 Se-Mets. In principle, I could use low res MR phases from the "replaced" model to locate Se-sites and then NCS-averaging to locate more sites and improve my phases. Any suggestions how to get Phenix to use an EM model? Has anybody done it successfully using Phenix? 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] Can Phenix do MR with medium/low res EM models?
by Thomas C. Terwilliger 19 Mar '09

19 Mar '09

Hi Gino, I have never tried any problem of this size...but here is a way to proceed using Randy's "input_partpdb_file" option for Phaser that is now available in the autosol wizard. Take your EM model with all its NCS copies, and give it to AutoSol with the keywords: input_partpdb_file=MR.pdb partpdb_rms= 3.0 The partpdb_rms should be the estimated RMSD between the MR model and the true model. You will have as good an idea about this as anyone... You also would supply the usual information to autosol: phenix.autosol sad-data.sca seq.dat 450 Se f_prime=-8 f_double_prime=4.5 \ build=False input_partpdb_file=MR.pdb\ partpdb_rms=3.0 \ resolution=6.0 You might cut the resolution to a pretty low value like 6 A as above. If you get a lot of good sites refined by phaser, then you may be on the right track. This autosol run will output phaser_1.mtz and also resolve_1.mtz that you can use as a starting point for further density modification and model-building as appropriate. Given the size of this problem, I would anticipate lots of challenges, and we will be happy to help as you carry on with it. You might try running everything at really low resolution (20A) at first just to get things to run... All the best, Tom T Hi Phenix community, I was wondering if Phenix can handle MR starting from medium/low res EM models. I have a very large oligomeric protein (2.4MDa) with lots of NCS and >450 Se-Mets. In principle, I could use low res MR phases from the "replaced" model to locate Se-sites and then NCS-averaging to locate more sites and improve my phases. Any suggestions how to get Phenix to use an EM model? Has anybody done it successfully using Phenix? 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

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omit maps without density modification?
by NATHAN THOMSEN 17 Mar '09

17 Mar '09

Hi, Is there is a way to calculate simple omit maps and sa-omit maps in phenix without using density modification? The density modification seems to be flattening the weaker regions of my map - when compared to omit maps from cns for instance. Thanks! Nathan

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AutoBuild error: csh word too long
by Zheng Zhou 16 Mar '09

16 Mar '09

Hi, All I am new to phenix. I met the following error when I run autobuild. I also found the following link from Dr. Lang asking the similar question. But I didn't find a clear solution. Thanks for your help. http://www.phenix-online.org/pipermail/phenixbb/2008-June/001087.html Starting job 1... ******************************************************************************** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /home/zz/AutoBuild_run_1_/TEMP0/RUN_FILE_1' Word too long. ******************************************************************************** Zheng

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Covalent ligands
by cdas＠purdue.edu 14 Mar '09

14 Mar '09

Greetings everyone: I have been dealing with a structure of a protein that has a Cys residue covalently modified with a peptide fluromethyl ketone. Can someone tell me how to include this ligand in phenix.refine? In the past, I have used CNS for this purpose. I created a topology and parameter file (using ProDrug server) and modified a patch in the refine script in CNS to establish a covalent connection between an atom in the ligand and gamma sulfur of the protein in question. Thanks. Chitta

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Beamtime proposal deadline for ALS GU time
by Peter Zwart 12 Mar '09

12 Mar '09

The deadline for the may/June cycle of general user time for PX in the ALS is coming up soon (This Sunday). The Berkeley Center for Structural Biology (BCSB) has recently completed a number of upgrades: Sector 8: Recent improvements 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 and the beamlines can be used remotely; * A new large format (315mm active surface area) CCD detector on BL 8.2.1 facilitates data collection on large unit cell crystals. Sector 5: Recent improvements include: * 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 (the 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 sector 5 beamlines can be run remotely. The automated sample mounter holds six pucks (96 sample in total). On weekdays, staff is available 22 hours (out of 24) for puck changes and assistance. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. If you'd like to apply for May/June beamtime at the Advanced Light Source, please submit a General User proposal by March 15, 2009. To find out more, click on: http://www-als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize. 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.] -- ----------------------------------------------------------------- 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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Re: [phenixbb] phenix.multi_crystal_average with twinned data
by Thomas C. Terwilliger 11 Mar '09

11 Mar '09

Hi Peter and Mary, For the cross-crystal averaging procedure, no refinement is done, so no problem about using detwinned data in phenix.refine. in this case. If detwinned data is supplied then it will be used for density modification. That is probably the best procedure at present. (Note that when running autobuild, you can input a specific "input_refinement_file" for refinement (raw data) and separately specify an input_map_file with a map and a data file with (optionally) detwinned data.) All the best, Tom T Hi, Detwinning is possible with xtriage or phenix.refine (on way or the other). Integrating this into density modification might be hard, especially when the twin fraction is high. What is your twin fraction? Tom, Is it possible to use a different set of amplitudes for density modification then for refinement? You wouldn't want to refine against detwinned data. Cheers Peter 2009/3/11 Thomas C. Terwilliger <terwilliger(a)lanl.gov>: > Hi Mary, > > I have not tried the phenix multi-crystal averaging procedure with > twinned > data, but here are some suggestions of how to proceed. > > 1. This routine does not do any refinement, only density modification. > The density modification step does not know about twinning, so it will > be > necessary (if your data are significantly twinned) to supply structure > factor files with detwinned data. I will check with Peter Zwart on > producing detwinned data in phenix; it may be necessary to do that with > other tools as normally phenix.refine uses the original data and does > the > calculations internally. > > 2. The models you supply are used to (a) identify NCS symmetry and > cross-crystal symmetry. Therefore it should not really matter if these > models are incomplete, and therefore the approach you are using should > work for improving the region where you have no model. The region where > NCS is applied is defined as a region centered near the center-of-mass > of > the supplied model over which the NCS correlation is high. > > > I hope that helps! > All the best, > Tom T > > > I started running this function and then realized that I probably need > to > do something to take the perfect twinning into account. I'm not sure of > the best way to do this. I believe the map coefficients output by a run > phenix.refine should be detwinned as I give a twin law when running > phenix.refine. Should I detwin the mtz containing the data and then use > those files for the multi crystal averaging? Is there a way to output > detwinned data mtz files in phenix or do I need to use another program? > > Also, I have two ncs copies in the ASU. There's a region of density in > both ncs copies that I'm trying to improve the maps for with the multi > crystal averaging. I don't have anything built in the region yet. Is > there a way to use the NCS and multi crystal averaging at the same time > without any pdb coordinates in that region? > > Even with my goof up about the twinning, the eff script I created > appeared to run without problems. > > Thanks, > > Mary X. Fitzgerald > Postdoctoral Associate > Arnold Lab > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > -- ----------------------------------------------------------------- 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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Re: [phenixbb] phenix.multi_crystal_average with twinned data
by Thomas C. Terwilliger 11 Mar '09

11 Mar '09

Hi Mary, I have not tried the phenix multi-crystal averaging procedure with twinned data, but here are some suggestions of how to proceed. 1. This routine does not do any refinement, only density modification. The density modification step does not know about twinning, so it will be necessary (if your data are significantly twinned) to supply structure factor files with detwinned data. I will check with Peter Zwart on producing detwinned data in phenix; it may be necessary to do that with other tools as normally phenix.refine uses the original data and does the calculations internally. 2. The models you supply are used to (a) identify NCS symmetry and cross-crystal symmetry. Therefore it should not really matter if these models are incomplete, and therefore the approach you are using should work for improving the region where you have no model. The region where NCS is applied is defined as a region centered near the center-of-mass of the supplied model over which the NCS correlation is high. I hope that helps! All the best, Tom T I started running this function and then realized that I probably need to do something to take the perfect twinning into account. I'm not sure of the best way to do this. I believe the map coefficients output by a run phenix.refine should be detwinned as I give a twin law when running phenix.refine. Should I detwin the mtz containing the data and then use those files for the multi crystal averaging? Is there a way to output detwinned data mtz files in phenix or do I need to use another program? Also, I have two ncs copies in the ASU. There's a region of density in both ncs copies that I'm trying to improve the maps for with the multi crystal averaging. I don't have anything built in the region yet. Is there a way to use the NCS and multi crystal averaging at the same time without any pdb coordinates in that region? Even with my goof up about the twinning, the eff script I created appeared to run without problems. Thanks, Mary X. Fitzgerald Postdoctoral Associate Arnold Lab _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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phenix.multi_crystal_average with twinned data
by Mary Fitzgerald 11 Mar '09

11 Mar '09

I started running this function and then realized that I probably need to do something to take the perfect twinning into account. I'm not sure of the best way to do this. I believe the map coefficients output by a run phenix.refine should be detwinned as I give a twin law when running phenix.refine. Should I detwin the mtz containing the data and then use those files for the multi crystal averaging? Is there a way to output detwinned data mtz files in phenix or do I need to use another program? Also, I have two ncs copies in the ASU. There's a region of density in both ncs copies that I'm trying to improve the maps for with the multi crystal averaging. I don't have anything built in the region yet. Is there a way to use the NCS and multi crystal averaging at the same time without any pdb coordinates in that region? Even with my goof up about the twinning, the eff script I created appeared to run without problems. Thanks, Mary X. Fitzgerald Postdoctoral Associate Arnold Lab

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