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xtriage output
by wtempel 02 Mar '12

02 Mar '12

Hello, this question is about the summary of xtriage output. I submitted merged scalepack intensity in space group P3. From scaling, the apparent point group is P622. H-tests for all three applicable twin laws indicate twin ratios around 45%. Does this merely indicate underestimated symmetry? STDOUT ends with this nugget: <stdout> The results of the L-test indicate that the intensity statistics Show more centric character than is expected for acentric data. </stdout> My questions: 1. What if anything should I infer about twinning from this last sentence? 2. What other data defects could this sentence indicate? Many thanks, Wolfram Tempel

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DEN refinement under phenix
by Melania Strycharska 02 Mar '12

02 Mar '12

Hi All, I was wondering whether anybody has successfully run the DEN refinement under phenix yet. I am having some problems with my scripts stalling without any error messages. What sort of reference models do people use? The following issues I am not quite clear on: - if I don't have a reference model should I call on my current pdb where the script calls for a reference model? - is it ok to use a single domain as a reference model or is it not enough to get the whole protein refined? - is it possible to use more than one reference model; in a case where I had structures of each domain solved separately? - can a reference model be a different protein or does it have to have the same sequence? Thanks a lot!

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Rfree refuse to come down
by #HEW KAI LI KELLY# 02 Mar '12

02 Mar '12

HI, I have a few questions about a dataset that I am working on currently. So I ran Xtraige and it tells me that other than pseudoNCS, there is no other problems like twinning etc. And then I used autoMR and Phaser from Phenix to run molecular replacement with a the structure of the same protein (but that is with DNA bound). The TFZ is more than 9 after from both the runs. Autobuild managed to build the 4 molecules in my ASU (Rfactor/Rfree = 28/32 for a resolution of 2.4A). But because there are some clashes and outliers in the Ramachandran Plot etc, I started to manually refine them in coot. In addition, there is a loop that is unable to fit into the density, so I chopped about 10 residues off each molecule in the ASU. However, as I started to refine the model from AutoBuild, my Rfree begins to climb. So currently, I am at Rfactor/Rfree=27/36. I don't know if there is anything wrong with I had done. So many thanks in advance for your advices on this!! Warmest Regards, Kelly Hew Nanyang Technogical University School of Biological Sciences Division of Structural Biology & Biochemistry Address : #07-01, IMCB, 61 Biopolis Drive, Proteos, Singapore 138673 Telephone (O): +65 65869673 Telephone (HP): +65 98713553

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Fwd: Hi Res Model. Maybe its time to Include Hydrogens?
by Yuri 02 Mar '12

02 Mar '12

Sue: I am not sure they are being included... I have the option checked, but the R values and difference maps tell me otherwise Pavel: A bug? That would be consistent with the behavior I observe. Even when I enable refinement with hydrogens individual or riding, i see essentially no difference in maps or Rfree values. -- Yuri Pompeu

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Hi Res Model. Maybe its time to Include Hydrogens?
by Yuri 02 Mar '12

02 Mar '12

Dear users, I am refining a 400 aa protein with data out to 1.16 A (real data). I am almost finished with refinement. I have good geometry, complete model and ligands Rw 0.11 Rf 0.13. Difference maps seem to be asking for more. See attached screen shot.Both maps 2Fo-Fc (non-filled) and Fo-Fc are contoured at 3 sigma. How should I handle this? I have used hydrogens all along (riding). Thanks for your time -- Yuri Pompeu

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phenix.reciprocal_space_arrays question
by Michael Thompson 01 Mar '12

01 Mar '12

Hi All, I have a very simple question about phenix.reciprocal_space_arrays. I apologize if this is obvious, but I could not find any info in the documentation or the bb archives. I just want to make sure that I am actually doing what I think I am doing. If I provide phenix.reciprocal_space_arrays with an .mtz file containing Fobs and a .pdb file for which I would like to calculate Fmodel and PHImodel, will the resulting Fmodel (and Fcalc, Fmask, Fbulk, etc.) be scaled to the Fobs from the input .mtz? Thanks for the help! Mike T. -- 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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BCA/CCP4 Summer School 2012
by Airlie McCoy 01 Mar '12

01 Mar '12

Applications are now open for the BCA/CCP4 Summer School in Protein Crystallography to be held at Diamond (UK) from Tuesday 28th August to Sunday 2nd September 2012. Applications close 1st May 2012. The BCA/CCP4 Protein Crystallography Summer School is intended for students and researchers new to crystallography. Its dual aims are to provide comprehensive training in crystallography and to promote best practise within the British crystallographic community. The lectures cover the gamut of techniques required for a structure solution, from protein expression through to structure validation. Intensively supervised computer tutorials enable students to relate the theory presented in the lectures to practice. Although CCP4 programs will primarily be used in these tutorials, the aim will be to approach crystallographic questions in a software-agnostic manner. There will also be a crystal manipulation and cooling workshop. (Note that the course is scheduled during Diamond synchrotron downtime, so there will not be active data collection at the Diamond beamlines.) For more information on eligibility, cost, and applications see: http://www.diamond.ac.uk/Home/Events/BCA-Summer-School-2012.html Application form: http://www.diamond.ac.uk/Home/Events/BCA-Summer-School-2012/Application-Pag…

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NCS-averaged and superposed maps
by Mullins, Elwood 29 Feb '12

29 Feb '12

Is it possible to both NCS-average and superpose maps? I can do one or the other easily enough from the command line (phenix.ncs_average) and the GUI (Superpose maps). Unfortunately, both programs require the input to be an mtz file but output ccp4-style maps. I don't see a way to do this sequentially. Is there some other method that would allow me to perform both operations? Thanks, Elwood =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elwood A. Mullins Ph.D. Candidate Department of Chemistry Washington University in St. Louis Campus Box 1134 One Brookings Drive Saint Louis, MO 63130-4899 Email: elwood.mullins(a)wustl.edu Tel: (765) 496-6814 Fax: (765) 494-7897 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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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 28 Feb '12

28 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 28 Feb '12

28 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 24 Feb '12

24 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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autoMR fixed ensemble error
by Alexander Batyuk 22 Feb '12

22 Feb '12

Dear all, I have the following error while trying to put fixed ensemble into AutoMR: Adding Ensemble c1 as fixed solution with: Euler angles: [359.98, 0.0, 0.0] Coords (orthogonal A): [-1.0, 0.476, -1.001] *************ERROR ENDING ******************* **************************************** AutoMR Input failed Python argument types in SOLU.addSOLU_6DIM_ENSE(InputMR_AUTO, str, list, bool, list, float, bool, bool, bool) did not match C++ signature: addSOLU_6DIM_ENSE(phaser::SOLU {lvalue}, std::string, scitbx::vec3<double>, bool, scitbx::vec3<double>, double, bool, bool, bool, bool, scitbx::vec3<double>, double) **************************************** *************ERROR ENDING ******************* What could be the reason for that? I'm running dev-986 on OS X 10.6.8. Stable 1.7.3 gives the same error. Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

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Re: [phenixbb] CCN Jan 2012 article : find_alt_origin_sym_mate
by R.D. Oeffner 22 Feb '12

22 Feb '12

Dear Bryan, The factor 0.9 is a purely empirical term. It serves two functions. One is to soften the minimas when atoms coalesce and to also prevent taking the logarithm of a negative number. The closer it gets to zero the more accurately it pinpoints the global minimum when the MLAD score is used for identifying the best superposition betweent two molecules. But if it becomes two small chances are that the landscape of MLAD values will be dotted with many very deep local minima which might lead to wrong results. The square boxes under the min, max symbols are typos to be ignored, sorry. There are currently no plans to publish further details about find_alt_origin_sym_mate. Regards, Robert Oeffner On Wed, Feb 15, 2012 at 4:33 PM, Bryan Lepore <bryanlepore at gmail.com> wrote: > will the find_alt_origin_sym_mate article in CCN Jan. 2012 be > described in any other publications? ... e.g. Acta Cryst., because I am interested in particular : 1. what is the significance of the factor of 0.9 2. is the MLAD a novel formula also, the 'min' and 'max' on p. 6 have small boxes under them [*] as if missing a character - are these integrals? -Bryan [*] tried evince and Adobe Reader on Linux, Adobe Acrobat on OSX 10.5.8 -- Robert Oeffner, Ph.D. Research Associate Department of Haematology, University of Cambridge Cambridge Institute of Medical Research Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY www-structmed.cimr.cam.ac.uk, tel:01223763234, mobile:07712 887162

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error in running autobuild
by intekhab alam 21 Feb '12

21 Feb '12

hi i am working with phenix version 1.7.1-743. after running auto mr i tried to run autobuild but it failed and generated the following message. i am unable to run autobuild now. kindly help. OError : [Errno 5] Input/output error Traceback (most recent call last): File "/usr/local/phenix-1.7.1-743/phenix/wxGUI2/Runtime.py", line 172, in OnUpdate self.propagate_event(event, "OnUpdate") File "/usr/local/phenix-1.7.1-743/phenix/wxGUI2/Runtime.py", line 228, in propagate_event fn(event) File "/usr/local/phenix-1.7.1-743/phenix/wxGUI2/Programs/Phaser/Output.py", line 194, in OnUpdate self.process_callback(callback.message, callback.data) File "/usr/local/phenix-1.7.1-743/phenix/wxGUI2/Programs/Phaser/Output.py", line 209, in process_callback print "CALLBACK: %s %s" % (str(message), str(data)) IOError: [Errno 5] Input/output erro -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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FFT map coefficients only for certain chains
by Zhang yu 20 Feb '12

20 Feb '12

Dear Phenixers, Is that possible to generate map coefficients only for certain chains? For example, I have two chains, A and B, and I would like to output a map file only contains coefficients for chain A. The "isomesh" command in Pymol could generate similar images. But my purpose is not for presentation, I need a map file only contains coefficient for certain chains. In the interface of "FFT" tool in Phenix or CCP4, there is an option to include a PDB file and define atom selections. It describe that "If a PDB is supplied, the output map will cover the model plus a buffer on all sides. The atom selection parameters can be used to specify a smaller region" . If I define the selection as chain A when I run the FFT, the output map still covers a rectangular block containing chain A, instead of regions only surrounding chain A. Thanks. Yu Zhang

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CCN Jan 2012 article : find_alt_origin_sym_mate
by Bryan Lepore 17 Feb '12

17 Feb '12

will the find_alt_origin_sym_mate article in CCN Jan. 2012 be described in any other publications? -Bryan

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MRage
by Graeme Winter 17 Feb '12

17 Feb '12

Hi Folks, Following from the newsletter article I am trying to test out phaser.MRage. I have a well solved case which I know is in the pdb and a sequence file: phaser.MRage hklin=data.mtz composition.component.sequence=sequence.pir symmetry_exploration=pointgroup mode=full search.services=ncbi composition.count=3 however it generates a second component then complains it knows nothing about this: Sorry: Molecular weight needed for component 2. Any suggestions how to get around this? Many thanks, Graeme [gw56@ws050 rage]$ phaser.MRage hklin=data.mtz composition.component.sequence=sequence.pir symmetry_exploration=pointgroup mode=full search.services=ncbi composition.count=3 ############################################################################### # MRage version 0.1.0 # ############################################################################### All configuration options: -------------------------- hklin = data.mtz labin = None resolution_cutoff = 2.5 crystal_symmetry { unit_cell = None space_group = None } mode = quick *full symmetry_exploration = *pointgroup enantiomorph dataset output { root = "mrage" max_solutions_to_write = 0 gui_base_dir = None save_aniso_data = False job_title = None } composition { count = 3 component { sequence = sequence.pir stoichiometry = 1 ensemble { coordinates { pdb = None identity = None } } model_collection { trim = False coordinates { pdb = None identity = None } } template { pdb = None alignment = None } homology { file_name = None max_hits = 3 } search { services = local ncbi max_hits = 3 } } component { sequence = None stoichiometry = 1 ensemble { coordinates { pdb = None identity = None } } model_collection { trim = False coordinates { pdb = None identity = None } } template { pdb = None alignment = None } homology { file_name = None max_hits = 3 } search { services = local *ncbi max_hits = 3 } } } queue { technology = lsf threading sge *multiprocessing pbs cpus = 1 submission_command = None qslot_cpus = 1 } packing_pool = 20 rotation_peaks_cutoff = 0.75 post_refinement_cutoff = 0.75 final_selection_cutoff = 0.75 b_factor_refinement = True significant_peak_threshold = 7.0 sculptor_protocols = 11 10 13 12 1 3 2 5 4 7 6 9 8 *all minimal template_equivalence = False exclude_pdb_ids = None simple_run { enable = False component_sequence = None template_model = None blast_services = local ncbi max_blast_hits = 3 } Sorry: Molecular weight needed for component 2.

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AutoSol with 4.2A dataset for a protein/DNA complex
by Wei Shi 17 Feb '12

17 Feb '12

Hi everyone, I have got a 4.2A SeMet MAD dataset for a protein-DNA complex. And, the native dataset for this protein-DNA complex is ~3.2A. The space group for the native and SeMet crystals seem to be different. I am not sure whether it’s possible to solve the structure with the current data I have, and wondering whether any of you have experience with working with this low-resolution data and any suggestion for me. I processed the data with XDS in space group P31, and used *.cns.hkl file from XDSCONV as an input for AutoSol and also include the sequence for protein only. The protein dimer has 418 residues and DNA is 32bp. I run Autosol with the default setting. Below is statistics I got. It seems that I didn’t get anything promising. Any comment or suggestion about what to try next? Thank you so much! Statistics: Top solution: 2 Sites: 11. Space group: P32. FOM: 0.550. BAYES-CC: 8.10. Residues: 465 Side-chains: 0. Chains: 60. Model CC: 0.67 R-work: 0.4100 R-free: 0.4569. Under Heavy-atom search and phasing: Space group # of refined sites FOM Overall score R-factor Map skew Corr. of local RMS density Solution1 P31 11 0.530 8.10+/-11.80 0.4184 -0.12 0.66 Solution2 P32 11 0.550 8.10+/-11.80 0.3881 -0.10 0.66 Best, Wei

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