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R-free flags
by 刘世恒 29 Feb '12

29 Feb '12

Hi, According to the phenix documentation, phenix.refine generates free R that are evenly distributed over the resolution, making sure that relatively thin resolution bins receive enough of reflections. The default behavior is to flag 5% of reflections up to a maximum of 2000. However,in some high-resolution structure, the percent for R-free test set which was generated by phenix.refine might be smaller than 1%， and it was a small percentage. Are there anticles related to the generation of R-free flag by phenix? Sincerely yours, Shiheng Liu

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adding solvents other than water
by Subhani Bandara 28 Feb '12

28 Feb '12

Hi all, How can I identify atoms like Na+, K+ in the map, from the positive density. Also can I add solvents like MPD and Tris buffer if any. Is there a specific way or do I have to run ligand fit. Is there any material I can read on this. Thanks in advance. Subhani

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Fixing ligand position in refine
by Christopher Wanty 27 Feb '12

27 Feb '12

Hi, I have a problem with a phosphate moving out of position during refinement. The complication is that there is an existing phosphate in the same location as the one I'm trying to place, but the existing one is part of a modified residue, and there is clearly density for the alternative conformation of the phosphate, but it is also clearly not still bound to the residue. How do I make sure that the phosphate does not move away from where it should be? Attached image show the phosphate more or less where I want it, and you should be able to see where the existing phosphate is attached to the residue. The large red density blob is where phenix.refine tried to put the phosphate last time. Kind regards, Chris ------------------------------------------------------- Dr. Christopher Wanty christopher.wanty(a)uwa.edu.au Research Associate Biomolecular, Biomedical and Chemical Sciences, Building M310 University of Western Australia 35 Stirling Highway Crawley 6009 Western Australia Australia

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MSE MET occupancy issue
by Ming 27 Feb '12

27 Feb '12

Hi all, I was trying to refine a protein with phenix.refine. I want to refine AMSE and BMET with occupancies 0.5 and 0.5. What I did is modifying the pdb file by copy the coordinates of MET to MSE, and change the names to be AMSE and BMET, modifying the occupancy to be 0.5 and 0.5 for each one. Everything else like the atom names have been taken care of too. I used the readyset to make sure the pdb file is good. But phenix.refine keeps giving me error saying "numbers of atoms with unknown nonbonded energy type symbols ". Anyone here can help me with this please? Thanks in advance,

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Phenix Error while running refinement
by Subhani Bandara 27 Feb '12

27 Feb '12

Hi everyone, I am getting following error while running phenix refinement for a protein cocrystalized with a metal chelator complex. What could be the problem. AssertionError : Traceback: File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/libtbx/thread_utils.py", line 229, in run return_value = self._target(self._args, self._kwargs, self._c) File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/libtbx/runtime_utils.py", line 72, in __call__ result = self.target() File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/phenix/phenix/refinement/runtime.py", line 67, in __call__ call_back_handler=callback) File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/phenix/phenix/refinement/command_line.py", line 97, in run call_back_handler=call_back_handler) File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/phenix/phenix/refinement/driver.py", line 1478, in run ncs_manager = self.ncs_manager) File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/phenix/phenix/refinement/strategies.py", line 344, in refinement_machine model.show_occupancy_statistics(text = "Occupancies statistics", out=log) File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/model.py", line 868, in show_occupancy_statistics self.xray_structure.set_occupancies(value=0., selection = less_than_zero) File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/cctbx/xray/structure.py", line 480, in set_occupancies assert selection.size() == s.size() Thanks Subhani

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mr problem and changed unit cell parameters
by intekhab alam 27 Feb '12

27 Feb '12

Hi all I have collected 2 datasets; one for the native proteins (2.3Å resolution) while other is for a protein-protein complex (3.5Å resolution). The unit cell parameters for the native are a=120, b=196, c=109, a=g=90, b=114, while for the complex data it is a=122, b=197, c=300, a=g=90, b=93. I have successfully got a MR solution and refined the native dataset with 3 monomers in the asymmetric unit. Analysis of the protein complex dataset shows 41% pseudo translation and so far there is no success in molecular replacement for this dataset. Can anyone please suggest me ways to solve this problem. i already have tried different templates like monomer, dimer, trimer, tetramer etc with truncations of loop region. i am using phaser, autoMR, molrep. Regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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Using a parameter file in GUI
by Subhani Bandara 24 Feb '12

24 Feb '12

Hi everyone, I need to input a parameter file describing the bond lengths of a metal chelator complex in my protein. I used a text file containing the commands with .params extension. when I add this file in GUI inputs in refinement, it gives a message "Phenix did not recognize the file type". What is the file type I should use? The file contained commands similar to the following with my metal and ligand atom names. refinement.geometry_restraints.edits { zn_selection = chain X and resname ZN and resid 200 and name ZN his117_selection = chain X and resname HIS and resid 117 and name NE2 asp130_selection = chain X and resname ASP and resid 130 and name OD1 bond { action = *add atom_selection_1 = $zn_selection atom_selection_2 = $his117_selection symmetry_operation = None distance_ideal = 2.1 sigma = 0.02 slack = None } bond { action = *add atom_selection_1 = $zn_selection atom_selection_2 = $asp130_selection symmetry_operation = None distance_ideal = 2.1 sigma = 0.02 slack = None } } Then I used command line to run "phenix.refine model.pdb data.mtz elbow.cif restraints_edits.params" it again gave error saying .params is an unknown file type. Am I doing anything wrong and is there any other way to fix the distances of the metal chelator complex. Thanks Subhani

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importing projects problem
by Haytham Wahba 23 Feb '12

23 Feb '12

i moved my project from computer to another i did import project under Files. i got my projects with all jop history but when i try to restor jop i get this report (see below) after that i see only .eff file under the input file, No .Sca or the pdb i used before. even the result of refinment is not there and refinment setting which i did not use. i tried to change the path in .eff file to the new location for .sca and .pdb but i did not help could you help me in that. thank you Haytham (((ImportError : No module named f_model_info Traceback (most recent call last): File "/usr/local/phenix-1.7-650/phenix/wxGUI2/Home/Jobs.py", line 327, in OnDoubleClick self.list_frame.restore_job(job) File "/usr/local/phenix-1.7-650/phenix/wxGUI2/Home/Jobs.py", line 241, in restore_job app.restore_job(self.project.get_id(), current_job) File "/usr/local/phenix-1.7-650/phenix/wxGUI2/App.py", line 544, in restore_job use_template_gui=use_template_gui) File "/usr/local/phenix-1.7-650/phenix/wxGUI2/App.py", line 501, in restore_session frame.restore_session(output_dir, config_file, result) File "/usr/local/phenix-1.7-650/phenix/wxGUI2/Programs/Refine/Main.py", line 473, in restore_session (result, last_status_file) = self._load_result_files(output_dir) File "/usr/local/phenix-1.7-650/phenix/wxGUI2/Programs/Refine/Main.py", line 467, in _load_result_files refine_result = easy_pickle.load(result_file) File "/usr/local/phenix-1.7-650/cctbx_project/libtbx/easy_pickle.py", line 21, in load return cPickle.loads(_open(file_name, "rb").read()) ImportError: No module named f_model_info)))

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question about phenix rosetta with two chains
by Elena Seiradake 23 Feb '12

23 Feb '12

Dear Phenixians, I would like to use mr_rosetta to re-build a model with two copies per AU. Although the two copies have the same sequence, they adopt different conformations and one is partially disordered. So I don't want to impose NCS. Could someone please send me an example input file for running mr_rosetta with phenix for multiple chains of the same protein? I think this probably would have to contain "fragment_files_chain_list" and "fragment_files_3_mer_by_chain" etc. (?) I have tried including the above keys in my script, in various ways, but I always get the error: "Sorry, the file path/test_1.pdb representing group 1 has no atoms? This could indicate a problem with sequence alignment in rebuilding" When I run it with just one of the two chains in my pdb (using simple "fragment_file ="), it rebuilds happily. Also, when use both chains and impose NCS=2 it works, but then one of the two chains is forced into the wrong conformation. Any advice on how to change my script would be welcome! Below is part of my simple script, the one that runs ok, using "fragment_file =". seq_file= Seq.dat \ data=test.mtz \ search_models=test.pdb \ already_placed=True \ fragment_files= frag_A_3.gz \ fragment_files= frag_A_9.gz \ rescore_mr.relax=False \ rosetta_models=20 \ ncs_copies= 1\ Cheers Elena

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composite omit map
by Ursula Schulze-Gahmen 22 Feb '12

22 Feb '12

I tried to calculate a composite omit map in autobuild for 3 complexes in the au. The calculation finished without any problems, but the maps look not right. There is density for the molecule, but there is a lot of density in the solvent areas, which I never saw when I calculated regular 2fo-fc maps or fo-fc maps. I also have calculated omit maps in autobuild before for single problem region and never saw anything like this. Any idea what could have gone wrong? Where should I start looking? Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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