September 2009 - phenixbb - phenix-online.org

Adding multiple conformers beyond 4
by Ben Mueller 15 Sep '09

15 Sep '09

I am a relatively new Phenix user and I am trying to see if it is possible to push the number of conformers beyond 4. I tried to do so, and I recieved the error message: RuntimeError: Exceed maximum allowable number of conformers (=4). Is there an easy (or difficult) way around this? Thanks for your time, Ben Mueller Phillips Lab Department of Biochemistry University of Wisconsin - Madison

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problems with kicked maps in phenix version 1.4-162
by Sabine Schneider 15 Sep '09

15 Sep '09

Hello, Im trying to generate kicked maps in phenix1.4-162 using the following comand: phenix.refine junk.mtz xray_data.labels=F_XDSdataset,SIGF_XDSdataset \ coot-1.pdb strategy=individual_sites simulated_annealing=true refine2.params where refine2.params is: electron_density_maps { map { mtz_label_amplitudes = 2FOFCWT_kick mtz_label_phases = PH2FOFCWT_kick 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_kick mtz_label_phases = PHFOFCWT_kick likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = true } } I get the following error message: refinement.input.xray_data.labels = F_XDSdataset,SIGF_XDSdataset refinement.refine.strategy = individual_sites refinement.main.simulated_annealing = true ******************************************************************************* ERROR: Unused parameter definitions: electron_density_maps.map.mtz_label_amplitudes (file "refine2.params", line 3) electron_density_maps.map.mtz_label_phases (file "refine2.params", line 4) electron_density_maps.map.likelihood_weighted (file "refine2.params", line 5) electron_density_maps.map.obs_factor (file "refine2.params", line 6) electron_density_maps.map.calc_factor (file "refine2.params", line 7) electron_density_maps.map.kicked (file "refine2.params", line 8) electron_density_maps.map.fill_missing_f_obs_with_weighted_f_model (file "refine2.params", line 9) electron_density_maps.map.mtz_label_amplitudes (file "refine2.params", line 12) electron_density_maps.map.mtz_label_phases (file "refine2.params", line 13) electron_density_maps.map.likelihood_weighted (file "refine2.params", line 14) electron_density_maps.map.obs_factor (file "refine2.params", line 15) electron_density_maps.map.calc_factor (file "refine2.params", line 16) electron_density_maps.map.kicked (file "refine2.params", line 17) electron_density_maps.map.fill_missing_f_obs_with_weighted_f_model (file "refine2.params", line 18) ******************************************************************************* Sorry: Unused parameter definitions: Please check the input file(s) for spelling errors and obsolete parameter definitions. To disable this error message, add --unused_ok to the command line arguments. I also tested the input file using : libtbx.phil refine2.params and it seems OK? Would be great if you could tell me where I am going wrong! Thanks a lot for your help in advance! Sabine -- ------------------------------------------ Dr. Sabine Schneider Ludwig-Maximilians-University Department of Chemistry and Biochemistry Butenandtstrasse 5-13, Building F 81377 Munich Germany Phone: +49 (0)89 2180 77752 Fax: +49 (0)89 2180 77756 http://www.carellgroup.de/

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A request
by Jonathan Grimes 15 Sep '09

15 Sep '09

Are there plans to implement STRICT NCS refinement in Phenix ?? For virus structures I am stuck with using CNS. Thanks Jon -- Dr. Jonathan M. Grimes, University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: Jonathan(a)strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

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omit map with phases
by Jianghai Zhu 14 Sep '09

14 Sep '09

Hi, When I am using phenix.autobuild to calculate an SA_omit map, I found out the phenix.autobuild automatically used the phases in my mtz file. How does phenix.autobuild use the phases? and is it a good idea to use phases in omit map calculation? and what kind of phases are preferred, experimental phases, phases after density modification, and phases after multi-crystal averaging? Thanks. -- Jianghai

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Using SAXS data for phasing at mediocre resolution.
by Francis E Reyes 14 Sep '09

14 Sep '09

Hi all I'm looking for anyone who has had (practical) experience using SAXS data to phase 4.2 A crystals. Please email me. 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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Sequence file for DNA
by jens j birktoft 12 Sep '09

12 Sep '09

Hi: What is the proper format for a sequence file for double stranded DNA duplex/helix ? Do both strands have to be entered, separated by >'s or just one of the complimentary strands Cheers Jay

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Phaser-Gui question
by Jonathan Grimes 11 Sep '09

11 Sep '09

Dear Developers, As a late developer I have recently started to use the new GUI. Its very impressive but what I would like to do is to fire off a number of jobs to vary parameters say in refinement or auto-rebuilding. I havent been able to work out how to submit multiple jobs via the same configuration tab window. Is this possible ? Am I missing a trick. Thanks Jon -- Dr. Jonathan M. Grimes, University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: Jonathan(a)strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

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SA omit map
by Pascal Egea 11 Sep '09

11 Sep '09

Dear All,I have a theoretical/practical question about omit maps and refinement. I am completing the refinement (in Phenix) of a protein-ligand complex at 1.3A resolution. I solved it by MR and automatic rebuilding of the protein alone first then built in the ligand. Rfree and Rfac are 19.4%/18.2% after TLS and water-picking in Phenix. The model includes everything protein, water, ligand and some ions. However I have some slight doubts one region in my ligand. What would be the best map, less biased, to look at this "very late" stage of the refinement. Are composite or systematic SA omit map useful options at this stage ? Thanks a lot in advance Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-825-1013 lab (310)-825-8722 email pegea(a)mednet.ucla.edu

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Re: [phenixbb] SA omit map
by Thomas C. Terwilliger 11 Sep '09

11 Sep '09

Hi Pascal, I think that if you are only concerned about one ligand then there are four overall options. The first, going back before you added the ligand, is likely to be the least biased, then the iterative-build omit, then the SA-omit and kicked maps. The iterative-build omit map is probably the best way to get rid of bias once it has been introduced, but it is also very computationally intensive. As you are only interested in the ligand, you probably do not need to do a composite map, saving you a lot of time. So the options are: 1. You can go back to the structure you had just prior to adding that ligand, and simply refine that structure and look carefully at the maps. As the structure has never seen the ligand, you have no worries about bias at all in that map. Of course that map may be from a much earlier stage, so it may not be so clear either...leading to the other options of.. 2. Take your current structure and run an SA-omit map or an iterative-build omit map, omitting around a PDB file that you create that contains only the ligand. 3. Or, pretty much equivalent to #2, you can remove your ligand from the structure and just do a run of SA or rebuild-in-place and calculate a map, 4. Or you can calculate a kicked map. For the kicked map, quoting Pavel Afonine: in your parameter file just add another map scope to the electron_density_maps scope, like this: electron_density_maps { map { mtz_label_amplitudes = "2FOFCWT_kick" mtz_label_phases = "PH2FOFCWT_kick" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = False } map { mtz_label_amplitudes = "FOFCWT_kick" mtz_label_phases = "PHFOFCWT_kick" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = False } } This will create two additional kick maps in addition to the default maps. All the best, Tom T , >> Dear All,I have a theoretical/practical question about omit maps and >> refinement. >> I am completing the refinement (in Phenix) of a protein-ligand complex at >> 1.3A resolution. I solved it by MR and automatic rebuilding of the protein >> alone first then built in the ligand. Rfree and Rfac are 19.4%/18.2% after >> TLS and water-picking in Phenix. The model includes everything protein, >> water, ligand and some ions. >> However I have some slight doubts one region in my ligand. >> What would be the best map, less biased, to look at this "very late" stage >> of the refinement. Are composite or systematic SA omit map useful options >> at this stage ? >> >> Thanks a lot in advance >> >> >> Pascal F. Egea, PhD >> Assistant Professor >> UCLA, David Geffen School of Medicine >> Department of Biological Chemistry >> 314 Biomedical Sciences Research Building >> office (310)-825-1013 >> lab (310)-825-8722 >> email pegea(a)mednet.ucla.edu >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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Auto builiding
by Jonathan Grimes 11 Sep '09

11 Sep '09

Dear Developers, I have a molecular replacement solution with a model that has 58 seq identity to my protein. There is 1 insertion in my protein of 1 residue and 1 deletion of 4 residues compared to the model. There are 2 mols in the asym unit. When I run autobuild with standard settings (but either Auto or Yes for the rebuild in place) it falls over with this error. **************************************** AutoBuild Input failed Sorry, the PDB file and sequence file could not be aligned (with no gaps and >50.0% identity) Please restart the wizard... You have several possibilities to try .... You can set rebuild_in_place=No You can set input_sequence_file=None You can edit your model to make sure it has no residues extending N-terminal of the beginning of the corresponding sequences in your sequence file You can set min_seq_identity_percent to a lower value You can set highest_resno to a higher value You can specify start_chains_list if your PDB file sequence starts with a residue number greater than the number of residues in the sequence. **************************************** It runs with rebuild_in_place=No but given the low resolution of the data (3.5A) I thought it would be best to keep as much of the model as possible. What am I doing wrong. Thanks Jon -- Dr. Jonathan M. Grimes, University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: Jonathan(a)strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

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