May 2011 - phenixbb - phenix-online.org

Problem with version 1.7.1-743 on OSX
by Miguel Ortiz Lombardía 06 Feb '12

06 Feb '12

Dear phenix developers, Last Friday (April 29) we upgraded phenix to its most recent version (1.7.1-743). Installation went smoothly on both Mac (10.6.7 64-bit) and Linux (Ubuntu 10.10 64-bit) machines. However, we observe that we cannot use phenix.refine (I don't know for the rest of the applications) from the GUI on the Macs. phenix.refine does work from the command line, though. So, whenever we try to add a pdb in the GUI, we get this error message: This application does not support the file type for /path/to/the/file.pdb (format: txt) If we try to open an mtz, it sometime works, but most often we get: PHENIX did not recognize the file type for /path/to/the/file.mtz! and on the terminal from where the GUI was started we can find: **SYMMETRY OPERATOR ERROR** Error in interpreting symop " X+2/3, Y+1/3, Z+1/3 " **SYMMETRY OPERATOR ERROR** Error in interpreting symop " -Y+2/3, X-Y+1/3, Z+1/3 " (and so on, so forth). Any clues ? Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:[email protected] http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Re: [phenixbb] ADP refinement selection
by Pavel Afonine 15 Jul '11

15 Jul '11

Hi Christian, the problem is that you did not ask phenix.refine to refine the rest of the atoms isotropically (with your command below you only refine anisotropic ADPs of atoms in chain Q, and the B-factors of all the other atoms are not refined): > adp { > individual { > anisotropic = "chain Q" > } I would do it like this: adp { individual { anisotropic = chain Q and element CL isotropic = not (chain Q and element CL) } } Pavel.

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scattering factors
by Goragot Wisedchaisri 21 Jun '11

21 Jun '11

Hi, I am new to Phenix but I have used Solve/Resolve in the past. I am currently using Phenix 1.6.2 and I have electron diffraction data to ~2A from a 300kV electron microscope that I would like to use Autobuild and phenix.refine to iteratively rebuild and refine my partial structure. I have a file containing electron scattering factors for 300kV EM that has been used successfully for refinement with CNS before for electron diffraction data. How can I tell Phenix to use electron scattering factors during refinement? I think currently Phenix has 4 choices for X-ray and neutron scattering factors but not for electron scattering. Is there a good way to implement electron scattering factors into phenix library? Any suggestions are welcome. George Wisedchaisri

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polygon Error.
by Yuri 07 Jun '11

07 Jun '11

Hello everyone, Keep getting an error when I try to run polygon to validate my model. Here is what i get: RuntimeError : lbfgs error: Line search failed: The step is at the lower bound stpmin(). Traceback: File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/libtbx/thread_utils.py", line 223, in run return_value = self._target(self._args, self._kwargs, self._c) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/libtbx/runtime_utils.py", line 58, in __call__ result = self.target() File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/phenix/phenix/validation/analyze_all.py", line 358, in __call__ result = validation_result(params, tmp_dir) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/phenix/phenix/validation/analyze_all.py", line 139, in __init__ return_fmodel_and_pdb=True) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/mmtbx/model_vs_data.py", line 806, in run mvd_obj.collect(model_vs_data = show_model_vs_data(fmodel)) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/mmtbx/model_vs_data.py", line 556, in show_model_vs_data sigmaa_plot = fmodel.sigmaa().show_short(silent=True) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/mmtbx/f_model.py", line 1464, in sigmaa use_sampling_sum_weights = p.use_sampling_sum_weights) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/mmtbx/scaling/sigmaa_estimation.py", line 191, in __init__ w_obs=w_obs) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/scitbx/math/chebyshev_lsq_fit.py", line 72, in __init__ self.minimizer = lbfgs.run(target_evaluator=self) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/scitbx/lbfgs/__init__.py", line 258, in run log) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/scitbx/lbfgs/__init__.py", line 143, in run_c_plus_plus if (minimizer.run(x, f, g)): continue Thank you -- Yuri Pompeu

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Re: [phenixbb] Refining sucrose
by Yuri 01 Jun '11

01 Jun '11

All coot needs to run its real-space refinement is a .cif file as Nigel pointed out. You can also get this file from other ligand library websites (proDrg, hic-cup, etc...). The only catch here is. The name of your sucrose atoms must match, exactly, those in the file. Once you have such file go to the the file drop-down menu and click on Import CIF dictionary in coot. That should enable to rotate the rotatable bonds of your ligand -- Yuri Pompeu

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ligand cif file
by ChenTiantian 01 Jun '11

01 Jun '11

Hi there, Now I use phenix.elbow to produce the cif file of the ligand instead of using Prodrg. but I find a problem with this cif file, the C=N bond is not right, it becomes C-N in the cif file, so it does not fit the electron density, what should I do to modify the cif file to chage C-N to C=N ? Best Regards, Tiantian -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

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mr_rosetta test failure
by Laurie Betts 31 May '11

31 May '11

We installed latest phenix and latest rosetta last week. I ran test script: phenix_regression.wizards.test_command_line_rosetta_quick_tests and got the test failing at the prerefine because of missing shared libraries, as shown below in the FAQ (italics). I tried again in both bash & csh after setting or exporting the environment variables shown below, but got the same exact error. If I do printenv the shell sees the new env var. What should I try next? THanks so much Laurie Betts & CD Poon University of North Carolina *Why does mr_rosetta bomb and say "error while loading shared libraries: libdevel.so: cannot open shared object file: No such file or directory ? This may indicate that somewhere your system is defining the shared libraries that Rosetta needs, and these are for a place that is not where Rosetta expects them to be. You can try to ignore the previous definitions this way: If you are using the bash or sh shells: export PHENIX_TRUST_OTHER_ENV=1 or csh (C-shell): setenv PHENIX_TRUST_OTHER_ENV 1 in the script where you run mr_rosetta, or before you run it from the command line. *

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Re: [phenixbb] strategy suggestion ???
by Michael Thompson 31 May '11

31 May '11

I once used the following strategy to search for ligands when the apo structure had already been determined. I was using Refmac at the time, but I don't see why you couldn't do it with phenix.refine. After you process your data, if your crystals with and without the ligands are isomorphous, then you don't necessarily need to do molecular replacement to get phases. After you process the data from your crystals with the ligands, you can take the mtz file and start refining with the pdb file for your apo structure. You can start with a rigid body refinement to account for any small shifts or rotations that may have taken place when you added the ligand. Then after that refine according to your protocol of choice. The main place you can run into trouble is if you have a polar space group. If you do the rigid body refinement and get a horrible R-factor, the there's a good chance you have indexed the two data sets in opposite orientations. This can be corrected by reindexing, I think the phenix tool for this is xmanip but someone can correct me if I'm wrong. Good luck, Mike ----- Original Message ----- From: "ChenTiantian" <chentiantian2010(a)gmail.com> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Monday, May 30, 2011 6:31:51 PM GMT -08:00 US/Canada Pacific Subject: [phenixbb] strategy suggestion ??? Hi, I just started learning crystallography months ago, and the software I used most is XDS, HKL2000, phenix and coot. Now I am working on a series of datasets-----the same target protein with various ligands. The following is my refinement workflow: 1, Processing data with XDS (or HKL2000 for some of the datasets) 2,Molecule replacement with phaser. 3,Check and modify the structure residue by residue with COOT, 4,phenix.refine with the following command line: phenix.refine protein.1.mtz protein.pdb \ strategy=individual_sites+individual_sites_real_space+individual_adp+tls \ simulated_annealing=true simulated_annealing.start_temperature=1000 \ simulated_annealing.cool_rate=10 main.number_of_macro_cycles=5 \ ordered_solvent=true refinement.input.xray_data.labels="F,SIGF" \ output.prefix=myprotein 5,Fit the ligand and redo step 3&4; stop refining when the Rwork and Rfree looks reasonable. 6,Chage the strategy line to strategy=individual_adp adp.individual.isotropic=all \ to remove the ANISOU lines in pdb file. Any suggestion for this workflow ? or how do you always deal with the similar case ? cause I'm new about this field,maybe I did something stupid. Ps, the value of Rwork and Rfree are too close, like, Final: r_work = 0.1741 r_free = 0.1817 bonds = 0.036 angles = 1.818 Is that reasonable ? -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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strategy suggestion ???
by ChenTiantian 31 May '11

31 May '11

Hi, I just started learning crystallography months ago, and the software I used most is XDS, HKL2000, phenix and coot. Now I am working on a series of datasets-----the same target protein with various ligands. The following is my refinement workflow: 1, Processing data with XDS (or HKL2000 for some of the datasets) 2,Molecule replacement with phaser. 3,Check and modify the structure residue by residue with COOT, 4,phenix.refine with the following command line: phenix.refine protein.1.mtz protein.pdb \ strategy=individual_sites+individual_sites_real_space+individual_adp+tls \ simulated_annealing=true simulated_annealing.start_temperature=1000 \ simulated_annealing.cool_rate=10 main.number_of_macro_cycles=5 \ ordered_solvent=true refinement.input.xray_data.labels="F,SIGF" \ output.prefix=myprotein 5,Fit the ligand and redo step 3&4; stop refining when the Rwork and Rfree looks reasonable. 6,Chage the strategy line to strategy=individual_adp adp.individual.isotropic=all \ to remove the ANISOU lines in pdb file. Any suggestion for this workflow ? or how do you always deal with the similar case ? cause I'm new about this field,maybe I did something stupid. Ps, the value of Rwork and Rfree are too close, like, Final: r_work = 0.1741 r_free = 0.1817 bonds = 0.036 angles = 1.818 Is that reasonable ? -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

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Inconsistent R-factors in PDB file
by Schubert, Carsten [PRDUS] 30 May '11

30 May '11

Hi, Not sure if this has been asked before but recently I noticed phenix seems to report inconsistent R-values after each refinement. The final values reported in the screen output after refinement match the values reported in the 'Quick Facts' section, but are not matched by the values in the PDB deposition section. Attached is an example: ... REMARK ******************** REFINEMENT SUMMARY: QUICK FACTS ******************* REMARK Start: r_work = 0.1907 r_free = 0.2151 bonds = 0.004 angles = 0.727 REMARK Final: r_work = 0.1838 r_free = 0.2141 bonds = 0.005 angles = 0.832 REMARK ************************************************************************ ... REMARK IF THIS FILE IS FOR PDB DEPOSITION: REMOVE ALL FROM THIS LINE UP. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (phenix.refine: 1.7.1_743) REMARK 3 AUTHORS : Adams,Afonine,Chen,Davis,Echols,Gopal, REMARK 3 : Grosse-Kunstleve,Headd,Hung,Immormino,Ioerger,McCoy, REMARK 3 : McKee,Moriarty,Pai,Read,Richardson,Richardson,Romo, REMARK 3 : Sacchettini,Sauter,Smith,Storoni,Terwilliger,Zwart REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.950 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.113 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.33 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.21 REMARK 3 NUMBER OF REFLECTIONS : 29410 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1894 REMARK 3 R VALUE (WORKING SET) : 0.1877 REMARK 3 FREE R VALUE : 0.2122 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.74 REMARK 3 FREE R VALUE TEST SET COUNT : 1982 For regular work I really don't care as long as the values are consistent and tell me if the refinement reached convergence, but for a deposition it matters a bit more. So which values should I report for a paper? Cheers, Carsten

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