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assertion error with autobuild (phenix 1.4.3)
by Jan Stout 04 Sep '09

04 Sep '09

Dear, I am trying to run the Autobuild Wizard to make a iterative-build omit map. I get the following errors after running Autobuild using the input file autobuild.eff generated by the wizard itself. I am working with phenix 1.4.3. Any input will be greatly appreciated. Many thanks, Jan Stout Traceback (most recent call last): File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/command_line/autobuild.py", line 339, in <module> run_autobuild=run_autobuild(args=sys.argv[1:]) File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/wizard_command_line.py", line 598, in __init__ self.RunWizard() File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/wizard_command_line.py", line 973, in RunWizard self.runWizard.run() File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/wizard_command_line.py", line 230, in run self.Wizard.Run(info='script') File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/AutoBaseExtend.py", line 726, in Run ok=self.CollectInputs()# raises AssertionError on failure File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/AutoBaseExtend.py", line 1790, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/wizards/AutoBuild.py", line 1074, in finish_AutoBuild_start all_files_ok=self.finish_Build_start() File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/BuildBase.py", line 382, in finish_Build_start all_files_ok=self.Build_finish_up_start() File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/BuildBase.py", line 508, in Build_finish_up_start str(self.Facts['input_data_file'])+"'") File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/UserMethods.py", line 84, in Error raise AssertionError,self.ErrorLine AssertionError: Sorry, cannot find the input_data_file ''

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question about phenix.refine
by crystallogrphy 04 Sep '09

04 Sep '09

Hi, I want to use phenix to refine a model right after autobuild with the following script: phenix.refine xray_data.file_name=exptl_fobs_phases_freeR_flags.mtz overall_best-090903a.pdb strategy=rigid_body+individual_sites simulated_annealing=true simulated_annealing.start_temperature=8000 sites.rigid_body="chain A" sites.rigid_body="chain B" However, the program says " F-obs: exptl_fobs_phases_freeR_flags.mtz:FP,SIGFP If previously used R-free flags are available run this command again with the name of the file containing the original flags as an additional input. If the structure was never refined before, or if the original R-free flags are unrecoverable, run this command again with the additional definition: refinement.input.xray_data.r_free_flags.generate=True when I use phenix.mtz.dump exptl_fobs_phases_freeR_flags.mtz, it indicates that it has FreeR_flag=1. Can anyone tell me why there is FreeR_flag in my data, while the refinement program does not recognize it? label #valid %valid min max type H 35619 100.00% 0.00 22.00 H: index h,k,l K 35619 100.00% 0.00 45.00 H: index h,k,l L 35619 100.00% -33.00 33.00 H: index h,k,l FP 35619 100.00% 0.00 114.22 F: amplitude SIGFP 35619 100.00% 0.15 6.13 Q: standard deviation PHIM 35619 100.00% 0.00 0.00 P: phase angle in degrees FOMM 35619 100.00% 0.00 0.00 W: weight (of some sort) FreeR_flag 35619 100.00% 0.00 1.00 I: integer FC 35619 100.00% 0.00 0.00 F: amplitude

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target omit map
by Susan Tsutakawa 03 Sep '09

03 Sep '09

I am trying to generate a simulated annealing omit map of a Mg-water cluster in the active site of my protein but when I run the SA omit map, I can only see the Mg when I use the Mgwater cluster as the target pdb. When I was building the model which did not have the metal present (phases solved by MR), I observed this Mg-water cluster in the Fo-Fc maps. Geometry and distance were ideal, etc. Now that I'm at the final stages of refinement, I would like to do a SA omit map as a figure for the paper. However, if I goto the lowest sigma, I only see the Mg. I'm using coot with the weights included to view the SA omit maps. I noticed that there is very little noise at the lowest sigma and so I'm wondering if the 0 sigma is truly 0 sigma and any suggestions on what to do. Thank you in advance. Sincerely, Susan

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reflection file utils : .cif?
by Bryan W. Lepore 03 Sep '09

03 Sep '09

[ phenix 1.4r3 cctbx tag: 2008_12_07_1353 intel-linux-2.6 redhat-e4.7 ] i obtained a recent .cif from the PDB, then run : phenix.reflection_file_converter --mtz=output.mtz test.cif file_name: test.cif file_type: None No reflection data found in input file. .... not sure where to go from here (a clip of the file is below, hope not too much) - i know i can run ccp4:cif2mtz, but are .cif part of phenix.reflection_file_converter? -bryan (sample of test.cif): data_testsf # _diffrn_radiation.id 1 _diffrn_radiation.pdbx_wavelength 1.00600 # _audit.revision_id 1_0 _audit.creation_date 2009-07-07 _audit.update_record 'Initial release' # _symmetry.Int_Tables_number 1 _symmetry.space_group_name_H-M 'P 1' # _cell.length_a 79.6610 _cell.length_b 104.1490 _cell.length_c 154.0250 _cell.angle_alpha 81.9570 _cell.angle_beta 75.9250 _cell.angle_gamma 73.7280 # _reflns.d_resolution_high 2.967 _reflns.d_resolution_low 46.392 _reflns.limit_h_max 26 _reflns.limit_h_min -25 _reflns.limit_k_max 34 _reflns.limit_k_min -34 _reflns.limit_l_max 51 _reflns.limit_l_min 0 _reflns.number_all 93210 _reflns.number_obs 85990 # loop_ _symmetry_equiv.id _symmetry_equiv.pos_as_xyz 1 'X, Y, Z' # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.status _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au 1 1 1 o -25 -16 1 218.4 77.9 1 1 1 o -25 -15 1 250.7 87.9 1 1 1 o -25 -15 2 217.9 78.8 (... etc... here is a free set hkl :) 1 1 1 f -25 -7 3 315.6 89.7 (... etc... until the end :) #END OF REFLECTIONS

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Custom Planar Restraints
by cheung＠lmb.uni-muenchen.de 03 Sep '09

03 Sep '09

Hi all - is it possible to specify custom planar restraints in phenix.refine? I'm refining a 3.8A protein-dna complex and although i've set hydrogen bonding restraints between base pairs, they still become very twisted and buckled after refinement. Alan

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question about autobuild
by crystallogrphy 03 Sep '09

03 Sep '09

Hi, I have used phenix.automr followed by phenix.autobuild to build a 264 residue model against my 2.1A resolution data set. The first run of autobuild gives me about 180 residues built. I have adjusted the model according to the denity. The N-terminal of the model has OK density to add more residues to the model. Can phenix.autobuild has some command to just put more residues to the N-terminal of my current model according to the density, so that the cost of CPU time will be much less than rerun the job completely? Thanks!

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Chain id of water is not reading by coot
by Raja Dey 02 Sep '09

02 Sep '09

Dear Friends, I have 7 chains in my pdb file. When I am reading the pdb file in COOT, for some reason the chain id(W) of water is not coming in the list. I clicked on 'draw' and then 'go to atom'. I can see all other chains but not W. I created water in PHENIX Is there any wrong in my pdb? HETATM 7562 O HOH W 542 -9.043 -2.133 -12.633 1.00 34.55 W O HETATM 7563 O HOH W 543 -22.004 8.228 -21.695 1.00 34.55 W O HETATM 7564 O HOH W 544 5.926 38.977 -11.538 1.00 34.55 W O HETATM 7565 O HOH W 545 -31.162 5.813 -31.403 1.00 34.55 W O Raja

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Improving picture quality of ED map in PYMOL
by Raja Dey 02 Sep '09

02 Sep '09

Dear Friends, Sorry, for the of topic question. Does anyone can tell how to improve the quality of a picture showing the electron density map of dna in a complex using PYMOL. I created the figure, but not happy with the quality as it is now. Might be there is a way to improve which I don't know. I want the lines in the mesh to be more sharp and fine. Any suggested program to prepare a publication quality figure to show the ED map would be of great help. Thanking you in advance... Raja

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Source for Nightlys Location?
by Andrew Ring 02 Sep '09

02 Sep '09

Is it possible to get a source distribution for the nightlys? If so, where is it located? I can only finding the builds on the nightlys downloads page. For my systems and uses, the --openmp switch on version 1.4-3 has given encouraging results and I would like to investigate with something newer. -- =================================== Andrew Ring System Administrator Kuriyan Laboratory http://jkweb.qb3.berkeley.edu/ Doudna Laboratory http://rna.berkeley.edu/ University of California, Berkeley Office: 542 Stanley Hall Shipping: 176 Stanley Hall, QB3 Berkeley, CA 94720-3220 tel: (510) 643 0166 fax: (510) 643 2352 ====================================

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R-work is too low
by Sam Stampfer 01 Sep '09

01 Sep '09

Hi, I'm refining a 2.88 Angstrom structure and am getting a difference of greater than 6% between the R-work and R-free. The best result (I think) is what I have from minimization alone: Start R-work = 0.3219, R-free = 0.3505 (no bulk solvent and anisotropic scale) Final R-work = 0.2424, R-free = 0.3174 (no bulk solvent and anisotropic scale) Start R-work = 0.3220, R-free = 0.3500 Final R-work = 0.2411, R-free = 0.3176 The results from simulated annealing are the following: Start R-work = 0.3219, R-free = 0.3505 (no bulk solvent and anisotropic scale) Final R-work = 0.2454, R-free = 0.3322 (no bulk solvent and anisotropic scale) Start R-work = 0.3220, R-free = 0.3500 Final R-work = 0.2403, R-free = 0.3333 I have also done the refinement with ncs but ncs is probably not appropriate for my structure. The final R-free ends up being higher (though the difference between R-free and R-work ends up being 6-7%) My PI (who is on vacation until next week) said that it was a problem if R-work was more than 0.06 lower than R-free. Any recommendations for me? Is it possible to reduce this difference? Is it worth it to rebuild the refined pdb if the R-work is this different from the R-free? My refinement script is: phenix.refine ss46_p3_cv.mtz ss46_rebuilt.pdb \ output.prefix=results/ss46_rebuilt_sa \ strategy=individual_sites+group_adp cif_link.params nag-nag.cif \ twin_law="h,-h-k,-l" \ simulated_annealing=true (the cif_link.params and nag-nag.cif files are made to handle the N-glycosylation sites, I think). Thanks for your help! -Sam

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