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Question about scale of ED maps from phenix vs map coeffs when displayed in COOT
by Schubert, Carsten [PRDUS] 21 Mar '09

21 Mar '09

Hi, Sorry for the crosspost, but I am not sure were the problem is located: I noticed that the xplor maps generated by phenix seem to be on a different scale than the maps generated from the map-coefficients from the same refinement run when the maps-coeffs are read into coot. Usually I only read in the map-coeffs and the scale seems reasonable to me, i.e. average density ~0.28 e/A3 at 1 sigma for a 2fofc map. The map from the same run (converted to ccp4 map in mapman) is at 0.55e/A3 at 1 sigma, when displayed in coot. The map should be normalized in phenix (apply_sigma_scaling=True) and the stats from mapman indicate an RMS deviation of ~1. For fofc maps I need to crank up the display to 6 sigma to get an equivalently looking map as the one from the map-coefficients at 3 sigma contour level. Any hints as to were the factor of 2 comes from, coot or phenix? Cheers, Carsten

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Problems with phasing a protein (1300aa)
by Kumar 20 Mar '09

20 Mar '09

Hello Phenixbb members, I have been trying to obtain phases for a protein which contain ~1300aa. We have obtained native data to a resolution of 3.3A (Space group I222 or I212121). But we are having tough time phasing it. 'Se' labeled crystals diffracts maximally up to 3.5 to 4 A and dies very quickly on most of the beamlines. We have scanned at Se wavelength and it gives very strong signal as it contain ~45 Se in AU (1300 aa). It is difficult to collect a complete dataset (maximally we get 50-60 % completion with Rmerge ~15) out of one crystal on regular beamline. At microfocus beamline (APS), we were able to collect data in 3-4 batches and merge them to get a complete dataset (Rmerge ~18-20) out of one crystal. We used data collected on microfocus beamline (at peak wavelength) for locating heavy atom position using SHELXD, Solve and Phenix.hyss. SOlve and Phenix.hyss find very few heavy atom sites 1-5 whereas SHELX-CDE lists many but shows no difference in original and inverted (contrast and connectivity). Our phasing attempts with datasets obtained after merging two incomplete dataset from two different crystal has also been disappointing. My another worry is absolute value of average intensity, which seems to be quite low in most of the datasets. Below I have pasted last table of scale.log (HKL2000). Shell Lower Upper Average Average Norm. Linear Square limit Angstrom I error stat. Chi**2 R-fac R-fac 50.00 7.53 45.4 1.6 1.3 1.295 0.055 0.047 7.53 5.98 11.4 1.3 1.3 0.672 0.135 0.114 5.98 5.23 11.2 1.6 1.6 0.643 0.171 0.152 5.23 4.75 16.8 2.0 1.9 0.736 0.148 0.118 4.75 4.41 18.8 2.2 2.2 0.739 0.143 0.132 4.41 4.15 14.6 2.4 2.4 0.653 0.190 0.175 4.15 3.94 11.3 2.5 2.5 0.582 0.247 0.226 3.94 3.77 10.1 2.8 2.8 0.511 0.280 0.191 3.77 3.63 8.0 3.1 3.1 0.450 0.315 0.285 3.63 3.50 7.6 3.3 3.2 0.483 0.311 0.270 All reflections 15.5 2.3 2.2 0.694 0.153 0.106 Now, I want you to help me by answering some of my queries: 1. Is it possible to get MAD/SAD phasing done from a dataset having more than 15% Rmerge and resolution in the range of 4 - 4.5 Ang? 2. Will a complete data set obtained from merging various batches(30-40 frames each) from one or more than one crystal will have proper anomalous signal for phasing? I am worried as weak anomalous signal may get lost while merging. 3. Will such a low value of average Intensities (as shown above from HKL scale log file) will be good enough for MAD/SAD phasing or I really need to improve crystal quality for stronger diffraction. 4. For MAD/SAD phasing, till what resolution we need to have anomalous signal ? Many of my datasets shows anomalous signal maximally up to 6-8 A (calculated using Phenix.xtriage). 5. Since I have low resolution (3.5 to 4 A)data, relatively high Rmerge (14-15%), lower value of average intensity, anomalous signal up to 6 A or so..... which programs will be more useful for heavy atom location and to prevent false positives from being selected? We have been also trying our luck with heavy atom soak but that also has not been very encouraging. I would appreciate any suggestions in this regard. Thanks in advance and sorry for such a long mail. Kumar

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question about generating cif and pdb file using elbow
by crystallogrphy 20 Mar '09

20 Mar '09

Hi, I am using phenix.elbow to generate pdb and cif files with the tripos format file: phenix.elbow --initial_geometry egcg.mol2 --opt --output="LIG" --pdb-ligand The input pdb file contains hydrogen atoms and the output pdb file also contains hydrogen atom. My crystal data only difftracted to 2.4A, so hydrogen atoms cannot be seen. In the refinement, my ligand should not contain hydrogen atoms. So I add one more option not to add hydrogen following the online phenix documentation: phenix.elbow --initial_geometry --write-hydrogens=False egcg.mol2 --opt --output="LIG" --pdb-ligand *However, the program failed. Does anyone know why?* Usage: phenix.elbow [options] *phenix.elbow: error: no such option: --write-hydrogens* -- Qun Wan Department of Pharmacology, Case Western Reserve University 10900 Euclid Avenue, Cleveland, OH 44106 email: qunwan1(a)gmail.com lab phone: 216-368-3337

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Problems with kicked maps in 1.4.3 or 1.4.4
by Schubert, Carsten [PRDUS] 20 Mar '09

20 Mar '09

Hi Pavel, I am having some problems with kicked maps. The job fails with a cryptic message: "Sorry Duplicate mtz_label_amplitudes: 2FOFCWT" and nothing gets written I noticed this in 1.4.3 a couple of days ago, just upgraded to 1.4.4, same problem. Running the same job w/o kicked maps enabled runs fine. Any ideas? Cheers, Carsten Here is a snipped of the .def file. output { prefix = "Prim_105_D6" serial = 4 serial_format = "%03d" write_eff_file = True write_geo_file = False write_def_file = True export_final_f_model = mtz cns write_maps = True write_map_coefficients = True } electron_density_maps { map_format = *xplor map_coefficients_format = *mtz phs suppress = None map { mtz_label_amplitudes = None mtz_label_phases = None likelihood_weighted = None obs_factor = None calc_factor = None kicked = False fill_missing_f_obs_with_weighted_f_model = True } map { mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = False fill_missing_f_obs_with_weighted_f_model = False } map { mtz_label_amplitudes = "FOFCWT_no_fill" mtz_label_phases = "PHFOFCWT_no_fill" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = False fill_missing_f_obs_with_weighted_f_model = False } map { mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = True } map { mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = True } anomalous_difference_map { mtz_label_amplitudes = "ANOM" mtz_label_phases = "PHANOM" } grid_resolution_factor = 0.25 region = *selection cell atom_selection = None atom_selection_buffer = 3 apply_sigma_scaling = True apply_volume_scaling = False }

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Re: [phenixbb] Can Phenix do MR with medium/low res EM models?
by Gino Cingolani 19 Mar '09

19 Mar '09

thanks Ed, I'll look it up.... I kind of tried something similar but never worked in my hands. I'll give it another try! By the way, the address of my house is 107 Ardsley Drive Dewitt 13214, NY. See you on Saturday 10 or so. Give me a call if you have problems 315 657 4805 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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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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