- phenixbb - phenix-online.org

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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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 21 Feb '12

21 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 20 Feb '12

20 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 19 Feb '12

19 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 16 Feb '12

16 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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Comprehension of Orotidine 5'-Monophosphate Decarboxylase
by Kevin Jin 15 Feb '12

15 Feb '12

Dear all, I wrote a story for Orotidine 5'-Monophosphate Decarboxylase. http://www.jinkai.org/Enzymology.html Best, Kevin

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Re: [phenixbb] qFit error in fixing alternate conformations
by Subhani Bandara 15 Feb '12

15 Feb '12

Hi, I used qFIT to fix the alternative conformations of my protein with a chelator complex, by submitting a PDB file and a mtz file. But it gave following error. What could be the reason for this. > > ___Run time error messages (if any):___ > xyz.pdb mtz.rfl FP SIGFP > Sorry: No matching array: refinement.input.xray_data.labels=FP,SIGFP > Thanks Subhani

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Re: [phenixbb] Example datasets
by mohamed noor 15 Feb '12

15 Feb '12

Dear Phenix users Is there some examples datasets involving 3-wavelength MAD phasing available? I would like to learn from indexing to structure solution with a combination of CCP4 and Phenix if possible. Thanks.

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cbf file
by Theresa H 15 Feb '12

15 Feb '12

Hi all Is there a utility to convert cbf file from Pilatus detector to mtz in Phenix? Thank you. Theresa

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Re: [phenixbb] alternative conformation of residues
by Subhani Bandara 14 Feb '12

14 Feb '12

Hi all, I have a protein where three consecutive amino acids have alternative conformations. I edited the PDB file to have those altloc and made total occupancy of A and B to 1.00. But after refinement both A and B are overlapping and I could see the positive density for one conformation away from that (may be b'se I didn't change coordinates of B conformation). How can I move the B altloc in to the positive density. Do I have to edit the coordinates on PDB and if so how can Ido that? Thanks in advance for any help Subhani

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problems when adding Free_R_flag
by G Y 14 Feb '12

14 Feb '12

Dear experts I use *Reflection file editor* in phenix GUI to generate Free_R_flag in my mtz file. The original input .mtz file contains arrays of FP SIGFP DANO SIGDANO and ISYM. I just simply click *COPY ALL ARRAYS* and tag on *Generation R free flags if not already present*, then run the software. The problem is that in the output .mtz from phenix I found the value of F and DANO becomes more or less same for each reflection. This is unreasonable for a reflection file. Phenix changed something on the columns of my .mtz file. How? Why? What should I do to keep my .mtz in correct and unchanged form? Thank you very much for your advice. The columns in the original input .mtz file look like H K L FP SIGFP DANO SIGDANO ISYM 0 0 12 319.30 2.64 2.23 5.27 0.00 0 0 16 424.00 3.50 -8.38 7.00 0.00 0 0 20 177.60 1.48 1.77 2.96 0.00 0 0 24 155.10 1.30 3.97 2.61 0.00 0 0 28 195.80 1.64 1.13 3.28 0.00 The output from phenix looks like (FP and DANO become similar in value for each reflection) H K L FP SIGFP DANO SIGDANO ISYM FreeRflag 0 0 12 320.41 3.73 318.19 3.73 0.00 0.00 0 0 16 419.81 4.95 428.19 4.95 0.00 0.00 0 0 20 178.48 2.09 176.72 2.09 0.00 0.00 0 0 24 157.09 1.85 153.11 1.85 0.00 0.00 0 0 28 196.37 2.32 195.23 2.32 0.00 0.00

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Computation Crystallography Newsletter
by Nigel Moriarty 14 Feb '12

14 Feb '12

Folks The latest issue of the Computational Crystallography Newsletter is available on-line at http://www.phenix-online.org/newsletter for download. The articles are of general interest to protein crystallographers and are listed below. Enjoy Nigel Moriarty Articles CCTBX tools for derivative-free optimization Short communications phenix.find_alt_orig_sym_mate Using force field generated models in the refinement of crystallographic structures containing carbohydrates Viewing diffraction images in CCTBX On contribution of hydrogen atoms to X-ray scattering -- Nigel W. Moriarty, Ph.D. Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Statistics from 'Scalepack' log file and 'Xtriage' log file
by Zhang yu 14 Feb '12

14 Feb '12

Dear Phenixer, What is the reason for the inconsistent data statistics from 'Scalpack' and 'Xtriage' ? I scaled my data with 'Scalepack' and got the following statistics (take completeness as an example) Shell I/Sigma in resolution shells: Lower Upper % of of reflections with I / Sigma less than limit limit 0 1 2 3 5 10 20 >20 total 40.00 8.93 0.1 0.2 0.4 0.9 1.5 22.6 97.3 0.0 97.3 8.93 7.10 0.8 1.7 2.7 4.1 7.1 35.8 99.2 0.0 99.2 7.10 6.20 2.0 4.6 7.6 10.9 18.4 56.6 99.5 0.0 99.5 6.20 5.64 2.9 6.5 11.1 16.3 27.5 65.0 99.0 0.0 99.0 5.64 5.24 4.1 8.2 13.7 19.2 33.0 67.3 97.4 0.0 97.4 5.24 4.93 4.3 9.4 14.8 19.9 33.1 67.6 96.1 0.0 96.1 4.93 4.68 5.2 10.1 15.9 21.8 33.9 67.8 95.6 0.0 95.6 4.68 4.48 5.4 11.2 17.6 24.7 37.8 69.0 94.5 0.0 94.5 4.48 4.31 5.8 11.0 18.1 25.1 39.8 71.2 94.0 0.0 94.0 4.31 4.16 6.4 14.3 23.6 32.7 47.2 73.6 93.7 0.0 93.7 4.16 4.03 8.2 16.7 27.2 36.7 53.0 76.5 93.1 0.0 93.1 4.03 3.91 9.3 20.5 32.4 42.6 57.8 79.1 93.5 0.0 93.5 3.91 3.81 9.6 23.1 37.2 47.7 61.4 81.6 93.6 0.0 93.6 3.81 3.72 11.6 26.5 41.3 51.7 66.1 84.5 92.9 0.0 92.9 3.72 3.63 11.6 30.9 47.8 58.4 71.0 86.5 93.7 0.0 93.7 3.63 3.55 14.9 34.4 50.7 62.0 74.3 88.9 94.5 0.0 94.5 3.55 3.48 15.4 37.1 54.7 64.6 76.2 89.5 93.4 0.0 93.4 3.48 3.42 17.2 41.5 60.1 69.4 79.6 90.8 94.0 0.0 94.0 3.42 3.36 18.3 44.6 62.3 70.9 79.7 89.4 92.1 0.0 92.1 3.36 3.30 20.8 46.9 64.2 71.9 79.7 88.3 90.3 0.0 90.3 All hkl 8.6 19.9 30.0 37.4 48.7 72.4 94.9 0.0 94.9 In summary, the overall completeness is 94.9%, while completeness of the lowest shell is close to 100%, and highest shell is 90.3%. But when I input the *.sca file into 'Xtriage', I got the following statistics (also completeness as an example). ---------------------------------------------------------------------------------------- | Res. Range | I/sigI>1 | I/sigI>2 | I/sigI>3 | I/sigI>5 | I/sigI>10 | I/sigI>15 | ---------------------------------------------------------------------------------------- | 40.02 - 8.19 | 51.1% | 50.9% | 50.7% | 50.2% | 38.9% | 5.1% | | 8.19 - 6.51 | 50.5% | 49.1% | 47.7% | 45.0% | 27.4% | 3.2% | | 6.51 - 5.69 | 49.0% | 45.7% | 42.9% | 37.1% | 18.0% | 1.4% | | 5.69 - 5.17 | 47.2% | 43.3% | 39.9% | 33.0% | 15.3% | 1.3% | | 5.17 - 4.80 | 45.8% | 41.6% | 38.4% | 31.6% | 14.6% | 1.2% | | 4.80 - 4.52 | 44.4% | 39.7% | 35.9% | 29.1% | 13.5% | 1.1% | | 4.52 - 4.29 | 43.4% | 38.2% | 33.6% | 26.4% | 11.5% | 0.8% | | 4.29 - 4.10 | 41.1% | 34.0% | 29.0% | 21.6% | 9.5% | 0.5% | | 4.10 - 3.95 | 36.1% | 29.2% | 24.6% | 18.5% | 7.6% | 0.3% | | 3.95 - 3.81 | 30.8% | 24.8% | 20.8% | 15.3% | 5.5% | 0.1% | | 3.81 - 3.69 | 27.4% | 21.6% | 17.7% | 12.4% | 3.8% | 0.0% | | 3.69 - 3.59 | 23.8% | 18.7% | 15.2% | 10.2% | 3.0% | 0.1% | | 3.59 - 3.49 | 20.3% | 15.5% | 12.6% | 8.3% | 1.9% | 0.0% | | 3.49 - 3.41 | 17.4% | 12.7% | 10.1% | 6.5% | 1.4% | 0.0% | ---------------------------------------------------------------------------------------- In summary, based on statistics from 'Xtriage', the data is quite incomplete, with only ~50% completeness even at lowest resolution shell. I convert the '*sca' into '*.mtz' file with "Reflection editor", and input the '*.mtz file' into 'Xtriage', I got another totally different statistics (completeness as an example) ---------------------------------------------------------------------------------------- | Res. Range | I/sigI>1 | I/sigI>2 | I/sigI>3 | I/sigI>5 | I/sigI>10 | I/sigI>15 | ---------------------------------------------------------------------------------------- | 39.67 - 8.19 | 96.5% | 96.2% | 95.8% | 94.9% | 74.0% | 10.0% | | 8.19 - 6.51 | 96.3% | 94.4% | 92.1% | 87.3% | 54.5% | 7.0% | | 6.51 - 5.69 | 92.6% | 88.1% | 83.3% | 72.7% | 36.2% | 3.5% | | 5.69 - 5.17 | 88.6% | 83.4% | 77.7% | 64.9% | 30.7% | 3.4% | | 5.17 - 4.80 | 85.6% | 80.0% | 74.8% | 62.3% | 29.4% | 3.3% | | 4.80 - 4.52 | 82.6% | 76.4% | 70.1% | 57.4% | 26.9% | 3.0% | | 4.52 - 4.29 | 80.6% | 73.4% | 65.7% | 52.3% | 23.2% | 2.2% | | 4.29 - 4.10 | 74.4% | 65.2% | 56.6% | 42.7% | 19.5% | 1.3% | | 4.10 - 3.95 | 64.2% | 55.7% | 48.2% | 36.7% | 15.5% | 1.0% | | 3.95 - 3.81 | 55.3% | 47.3% | 40.8% | 30.4% | 11.2% | 0.4% | | 3.81 - 3.69 | 48.7% | 40.9% | 34.7% | 24.8% | 8.1% | 0.2% | | 3.69 - 3.59 | 41.8% | 35.8% | 29.7% | 20.2% | 6.1% | 0.1% | | 3.59 - 3.49 | 35.3% | 29.4% | 24.5% | 16.6% | 4.1% | 0.0% | | 3.49 - 3.41 | 30.1% | 24.1% | 19.8% | 13.2% | 2.9% | 0.0% | ---------------------------------------------------------------------------------------- I am confused by the inconsistent statistics, could some explain it? Thanks. Yu

4 7

(no subject)
by intekhab alam 10 Feb '12

10 Feb '12

Hi all I have a 3A dataset for a protein-protein complex. I have successfully build the first protein and refined it to R/Rfree 24/28. I can see some density for my second protein but the density is a bit noisy. I have attached the coot image of the density. I want to model the aminoacid having sequence as given peptide: MGKKGKNKKGRGRPGVFRTRGLTDEEYDEFKKRRESRGGKYSIDDYLADREREEELLERDEEEAIFGDGFGLE 1.Based on map features which segemnt should i start with. 2. Is there anyway that i can build the best fit segment of my second protein. I tried autobuild but it failed to build any peptide for my second protein. Your help is highly appreciated. regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

3 2

phenix.ready_set
by Jianghai Zhu 10 Feb '12

10 Feb '12

Hi, I am using phenix.ready_set (version 1.7.3) to add hydrogens to my structure. I found out that it makes a few mistakes when dealing with glycans. It adds hydrogens to C1, O4, O3, O6 even when these atoms have formed covalent bonds with other sugars and residues. Subsequent phenix.refine aborts because of these incorrect hydrogens. However, when I use phenix.reduce directly, all hydrogens are placed correctly. I assume something went wrong in phenix.ready_set. The problem with phenix.reduce is that it doesn't know how to deal with ligand whereas phenix.ready_set does when a cif file is provided. -- Jianghai

5 6

sa_omit map calculation
by Ursula Schulze-Gahmen 08 Feb '12

08 Feb '12

I want to calculate a sa-omit map around the same small region in the 3 molecules in the au. I have 2 questions: Can I include the 3 regions in the same omit box file? What does the following advice in the manual mean: (Note: be sure to use the weights in both resolve_composite_map.mtz and omit_region.mtz). I am not sure what weights we are talking about? Thanks for any help. Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

2 1

Assigned occupancy refinement
by Fischer 08 Feb '12

08 Feb '12

Hello PhenixBB, We are interested in refining 3 distinct backbone conformations of a loop (A, B, C). Our crystals are very high resolution and the density is fairly distinct for each of these conformations. In the simplest case - each individual backbone conformation has one residue in two alternative side chain conformations. (A1,A2; B1,B2; C1,C2). We'd like to keep each pair of conformations assigned to the respective loop and then refine all six occupancies. Is there such an option similar to the free parameters in shelx also available in phenix? Thanks, Marcus

2 1

Rosetta Fragment viewer
by 商元 08 Feb '12

08 Feb '12

Dear all, Is there any program that can view the fragment files generated from Rosetta Fragment library? For example, I want to build a model myself, and I know the secondary structure of the target protein, so I will dock the 9-fragment myself. But, at the first step, I have to choose one fragment from the Rosetta fragment library generated. So, I wish if I can find any program that integrate the 200 9ers at specific position together, and then choose a good model by the shape I wanted. Did anyone here know such a program? Best Regards, Yuan SHANG

1 0

phenix.table_one
by Hasan Demirci 07 Feb '12

07 Feb '12

Hi, I am running phenix-dev-978 (fedora core 15 installer) version on a quad core intel chip computer. How can I obtain a table without digging a lot of files? When I use command line and try to run phenix.table_one I am getting the following AssertionError message: Is it a mistake in the input files or is it a bug in this version of phenix I am using? Thanks. ------------------------------------------------------------------------------- phenix.table_one f71c_refine_006.pdb outputf71c.mtz note: this is somewhat difficult to configure on the command line at present; you may find it more convenient to use the PHENIX GUI. Attempting to guess labels for outputf71c.mtz... Attempting to guess R-free label for outputf71c.mtz... #Final effective parameters: table_one { structure { name = None pdb_file = "f71c_refine_006.pdb" mtz_file = "outputf71c.mtz" data_labels = "IMEAN_wt30Sapo,SIGIMEAN_wt30Sapo" r_free_flags.label = "FREE" log_file = None cif_file = None cif_directory = None data_type = *xray neutron } processing { parallel = False re_compute_r_factors = False } multiprocessing { enable_multiprocessing = True method = *mp sge nproc = 1 tmp_dir = None } output { directory = "/home/Demircha/Desktop/test" job_title = None show_missing_fields = True format = *txt csv *rtf base_name = "Table1" verbose = "True" text_field_separation = 2 } } #---end Running phenix.model_vs_data for all structures. . . Multiple segs ' ' 12 'A ' 12 Use --do-all to process all residues not in internal library Traceback (most recent call last): File "/xsoft/phenix-dev-978/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/table_one.py", line 7, in <module> use_current_directory_if_not_specified=True) File "/xsoft/phenix-dev-978/phenix/phenix/automation/table_one.py", line 424, in run out=out).collected_stats File "/xsoft/phenix-dev-978/phenix/phenix/automation/statistics.py", line 173, in __init__ results.append(run_model_vs_data(structure)) File "/xsoft/phenix-dev-978/phenix/phenix/automation/statistics.py", line 93, in run_model_vs_data log=null_out()) File "/xsoft/phenix-dev-978/cctbx_project/mmtbx/model_vs_data.py", line 744, in run mmtbx_pdb_file.set_ppf(stop_if_duplicate_labels = False) File "/xsoft/phenix-dev-978/cctbx_project/mmtbx/utils.py", line 1819, in set_ppf silent=True, File "/xsoft/phenix-dev-978/elbow/elbow/scripts/elbow_on_pdb_file.py", line 2310, in run model_vs_data=model_vs_data, File "/xsoft/phenix-dev-978/elbow/elbow/scripts/elbow_on_pdb_file.py", line 732, in elbow_on_pdb_file molecule = extract_polymer_unit(pdb_inp, molecule, code) File "/xsoft/phenix-dev-978/elbow/elbow/scripts/elbow_on_pdb_file.py", line 213, in extract_polymer_unit if residue_group.resseq.strip() == molecule.GetSequenceID().strip(): continue File "/xsoft/phenix-dev-978/elbow/elbow/chemistry/SimpleMoleculeClass.py", line 1575, in GetSequenceID assert 0 AssertionError

3 2

Composite Omit Map Calculations - Batch Que
by Matthew J. Whitley 07 Feb '12

07 Feb '12

Hello all, I usually set up simulated annealing composite omit map calculations via the Phenix GUI and set the number of processors equal to 2 to take advantage of my Mac's dual core processor in order to shorten the calculation time somewhat. My department does have a high performance cluster, however, and I would like to start using that multi-node system to shorten the calculation time substantially. The problem for me is that the high performance cluster requires jobs to be submitted and managed via a PBS queue. I know how to specify in the PBS shell script the computing resources I want to use (say, for example, 8 dual core processors for a total of 16 nodes). My question is, do I need to specify any additional settings in the actual Phenix command line execution statement? For example, nproc = 16? Anything else? The entire shell script containing the PBS setup statements and the actual Phenix execution statements is submitted by the qsub command. In essence, I am wondering how to get Phenix to "play nicely" with the queueing system such that the composite omit calculations will be distributed box by box over the resources I reserve via the PBS statements. Thanks in advance for any advice. Also, if anybody has experience running Phenix jobs via a shell script submitted to a batch queueing system, I would very much appreciate the chance to look at the shell script. Thanks, Matthew --- Matthew J. Whitley, Ph.D. Postdoctoral Research Fellow Angela Gronenborn Lab Department of Structural Biology University of Pittsburgh School of Medicine

2 1

Difference in water molecules count
by bsubedi＠btk.fi 07 Feb '12

07 Feb '12

Hi All, I have been refining the mutant structures and at the end while making the comparative study I found that there is a large difference (almost half) number of water molecules in the protein strucutre of same mutant from different crystal conditions. The resolution of the structure, space group and no.of molecules in a.s.u is same. Here is the data collection statistics and no.of water & protein atoms present. I could also not understand the difference of unique and measured reflections at same resolution. Could anyone please explain me? Resolution range (Å) 20-1.6 (1.64-1.60) 20-1.8 (1.85-1.80) 20-1.9 (1.99-1.94) 20-1.6 (1.63-1.59) 20-1.6 (1.64-1.60) Number of measured reflections 221864 (14118) 173933 (9556) 85976 (5129) 206723 (12667) 262291 (15803) Unique reflections 84896 (6139) 59955 (4010) 38628 (2777) 86161 (5992) 85305 (5803) Completeness (%) 98.7 (97.2) 95.9 (87.9) 77.6 (75.5) 93.9 (87.9) 97.8 (90.9) No of protein atoms 5101 5096 5076 5113 5120 No of waters 1103 528 453 585 1214 Thanx, World

2 3

CASP Roll: Call for novel fold and membrane protein targets to help improve structure modeling methods
by Torsten Schwede 06 Feb '12

06 Feb '12

Dear colleagues, As many of you know, the CASP community experiments have been running once every two years since 1994, collecting information on soon to be solved structures from the experimental community, and passing on sequence data to the structure modeling community so that blind predictions of structure can be collected and assessed (1). Over that period CASP has seen enormous progress in the quality of modeled structures (2), but many problems remain. The regular CASP experiments collect target information for a three month season every two years, and in that period, thanks especially to the structural genomics community, can acquire over 100 targets, sufficient to evaluate the state of the art for most types of template based modeling. There are some classes of target, specifically proteins with novel folds and membrane proteins, where there are not enough structures solved in three months to provide sufficient information so the methods can be fully evaluated. As a consequence, progress is slowed. To address this problem, with the encouragement of the modeling community, CASP has launched a rolling mechanism, where we accept targets in these categories at any time. Of course for that to work we rely on you, the experimentalists, to provide suitable targets! So we are asking that you tell us about structures in these categories that are about to be solved whenever they come up. For those of you who have not provided targets to CASP before, the procedure is simple – there is a web page for submitting targets, and a very experienced staff to deal with any queries. We don’t need the structure in advance of its release by the PDB, and if we are notified early enough (a minimum of three weeks before release, more is better) there need be no delay in structure release. If you have a suitable target now, we are up and running with 50+ prediction teams already submitting models, and would love to have your targets. Most important, the modeling community is now in continuous need of your assistance, so please get in touch whenever an opportunity arises in the future, and help improve modeling methods. Thanks, CASP organizing committee John Moult, IBBR, University of Maryland, USA Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis, USA Torsten Schwede, University of Basel & SIB, Switzerland Anna Tramontano, University of Rome, Italy Get in touch: casp(a)predictioncenter.org More information: http://www.predictioncenter.org/casprol/ CASP Roll targets so far: http://www.predictioncenter.org/casprol/targetlist.cgi Submit a target: http://www.predictioncenter.org/casprol/targets_submission.cgi 1. Critical assessment of methods of protein structure prediction (CASP)--round IX. Moult J, Fidelis K, Kryshtafovych A, Tramontano A. Proteins. 2011;79 Suppl 10:1-5. doi: 10.1002/prot.23200. Epub 2011 Oct 14. 2. CASP9 results compared to those of previous CASP experiments. Kryshtafovych A, Fidelis K, Moult J. Proteins. 2011;79 Suppl 10:196-207. doi: 10.1002/prot.23182. Epub 2011 Oct 14.

1 0

FW: Summer Internship at Merck for Ph.D. students
by Soisson, Stephen M 06 Feb '12

06 Feb '12

All, We have a summer internship opening at Merck (see below for the details) for graduate students in the Global Structural Chemistry/X-ray crystallography/Biomolecular NMR group at either its Kenilworth, NJ or West Point, PA sites. Internships will begin in early June 2012, and will run for 10-12 weeks. If you are interested please visit our career site at www.merck.com/careers<http://www.merck.com/careers> to create a profile and submit your resume for requisition #CHE003379. Sincerely, Steve Soisson -------------- Job Description X-ray Crystallography/BioNMR Summer Internship 2012 - PhD:CHE003379 Description Merck is a global health care leader with a diversified portfolio of prescription medicines, vaccines and consumer health products, as well as animal health products. Today, we are building a new kind of healthcare company - one that is ready to help create a healthier future for all of us. Our ability to excel depends on the integrity, knowledge, imagination, skill, diversity and teamwork of people like you. To this end, we strive to create an environment of mutual respect, encouragement and teamwork. As part of our global team, you'll have the opportunity to collaborate with talented and dedicated colleagues while developing and expanding your career. Merck Research Labs will be offering 2012 summer internships in the Global Structural Chemistry group (X-ray crystallography or Biomolecular NMR) at either its Kenilworth, NJ or West Point, PA sites. Internships will begin in early June 2012, and will run for 9-11 weeks. A suitable candidate has a science background with interest in the use of X-ray crystallography and/or Biomolecular NMR in drug discovery. Not required, but a plus, would be experience in one or more of the areas of protein crystallization, X-ray theory, X-ray crystallography or Biomolecular NMR. Preference will be given to candidates having a strong math and/or physical science background with expertise in computers and computer programming. Candidates will gain firsthand experience in modern drug discovery, and will also make valuable contacts within the industry. **Please note when applying for this position, the candidate MUST upload a cover letter or a personal statement letter and a copy of your unofficial transcript along with your resume. Qualifications Required: * Currently pursuing a Ph.D. in Biomolecular NMR, X-ray crystallography, Computational Chemistry, Biophysics or a related field * Applicants must be available for full-time employment for 9 - 11 weeks during the months of June - August 2012. Preferred: * Experience in one or more of the areas of protein crystallization, X-ray theory, X-ray crystallography or Biomolecular NMR * Strong math and/or physical science background with expertise in computers and computer programming * Science background with an interest in computers and drug discovery Our employees are the key to our company's success. We demonstrate our commitment to our employees by offering a competitive and valuable rewards program. Merck's benefits are designed to support the wide range of goals, needs and lifestyles of our employees, and many of the people that matter the most in their lives. To be considered for this position, please visit our career site at www.merck.com/careers<http://www.merck.com/careers> to create a profile and submit your resume for requisition #CHE003379. Merck is an equal opportunity employer, M/F/D/V - proudly embracing diversity in all of its manifestations. Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

1 0

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.

6 12

Illegal instruction (core dumped)
by Hasan Demirci 04 Feb '12

04 Feb '12

Hi Folks, I just finished updating phenix-dev-944 to phenix-dev-975 version on Fedora Core 16 OS intel quad-core machine. When I run phenix from terminal "phenix.refine" I am receiving the following error message "Illegal instruction (core dumped)". This is the first time I saw this error. All the other programs run fine except phenix. I downloaded and installed it twice to see if it was an error of download but it still gives the same message. Is it an installation error or is it a bug in this version? Thanks. -- Hasan DeMirci

2 7

MAD from many crystal
by Theresa H 03 Feb '12

03 Feb '12

Hi everyone. Can I do 3 wavelength MAD phasing with AutoSol GUI with data from multiple crystals? Is there a reference/guide that I can use? Thank you. Theresa

4 5

structure comparison
by Christian Roth 03 Feb '12

03 Feb '12

Hi all, I tried the structure comparison in phenix validation and loaded seveeral structures and a sequence file. I started and than this strange error appears Did I specified something wrong? Best Regards Christian AssertionError : Traceback: File "/userdata-2/christian/phenix- dev-968/cctbx_project/libtbx/thread_utils.py", line 229, in run return_value = self._target(self._args, self._kwargs, self._c) File "/userdata-2/christian/phenix- dev-968/cctbx_project/libtbx/runtime_utils.py", line 72, in __call__ result = self.target() File "/userdata-2/christian/phenix- dev-968/phenix/phenix/automation/structure_comparison/__init__.py", line 1041, in __call__ analyses = run(args=list(self.args), log=sys.stdout) File "/userdata-2/christian/phenix- dev-968/phenix/phenix/automation/structure_comparison/__init__.py", line 1006, in run analyses = manager(params.structure_comparison, log=log) File "/userdata-2/christian/phenix- dev-968/phenix/phenix/automation/structure_comparison/__init__.py", line 196, in __init__ self.run() File "/userdata-2/christian/phenix- dev-968/phenix/phenix/automation/structure_comparison/__init__.py", line 250, in run self.process_alignment() File "/userdata-2/christian/phenix- dev-968/phenix/phenix/automation/structure_comparison/__init__.py", line 370, in process_alignment log=self.log) File "/userdata-2/christian/phenix-dev-968/cctbx_project/mmtbx/msa.py", line 262, in align_pdb_hierarchies assert (reference_hierarchy is None)

2 1

Re: [phenixbb] [ccp4bb] Lysozyme/Xenon derivatives & Phenix.
by Randy Read 03 Feb '12

03 Feb '12

Hi, I'm cross-posting this to the Phenix-BB, because you did this calculation in Phenix, but since the site completion for SAD phasing would be done with Phaser, the answer is relevant to both packages. Basically, I think Jim Pflugrath's suggestion is correct. Comparing your Xe coordinates to S and Cl coordinates from one of our test SAD phasing datasets, the majority of your extra sites are in the positions of either intrinsic S anomalous scatterers or bound halides. The Phaser completion step found them, even though you only asked for 2 sites initially, because it continues adding new sites as long as there are significant peaks in the SAD LLG maps. The refined occupancies make sense, assuming you were collecting your data around 1A wavelength. At that wavelength f" is about 4-5e for Xe and about 0.25-0.3 for S or Cl, and multiplying (say) 4.5e by occupancies of 0.03-0.08 gives effective f" values of 0.14-0.36e. Of course, Phaser isn't just trying to fit the imaginary part of the scattering, so the occupancies could end up slightly higher because it's trying to account for atoms with 16-17 electrons using partially-occupied atoms with 54 electrons. Knowing that, once Phaser has found the Xe atoms, it will then find the weak anomalous scattering from S and Cl, you could tell Phaser to look in addition for S atoms. (At around 1A wavelength, there's not enough difference between S and Cl, in either their real or anomalous scattering, to matter, so you don't need to look for Cl in addition.) Phaser will reassign atom types based on refined occupancy, so it would likely get most of these right, which would very slightly improve your phasing model (because you would then have the right ratio of real to imaginary scattering). Another advantage to looking for both atom types is that, when you mix atoms with different ratios of real and imaginary scattering, Friedel's law is broken even for the substructure structure factors, which has two consequences. First, the likelihood score will probably be significantly better for the correct enantiomorph than the incorrect one; second, you're likely to end up with a slightly more complete substructure when working with the correct enantiomorph. Note that AutoSol also chose the correct enantiomorph after phasing, by looking at map quality indicators for the two hands. Regards, Randy Read On 2 Feb 2012, at 16:43, Brennan Bonnet wrote: > Hi all, > > I have a strange result using Phenix's AutoSol to look for xenon sites in lysozyme. > > For a few months now I have been trying to produce xenon derivatives of lysozyme using pressures in the range of 50-350psi and time ranges between 5-60min trying to find the "sweet spot" so that this technique can be applied to other proteins. > > For each dataset, I AutoSol using phenix and have it look for 2, 3, and 4 xenon sites. I haven't had much success though and typical values when asked to look for 2 sites have been Rwork/Rfree = 0.5585/0.5892, CC=0.14, Bayes-CC=6.5 and with xenon sites: > > (a, b, c, alpha, beta, gamma, space group) > CRYST1 78.870 78.870 36.940 90.00 90.00 90.00 P 41 21 2 > > (columns after numbering are a, b, c, occ, B factor) > HETATM 1 XE XE Z 1 48.601 67.475 1.088 0.06 6.58 XE > HETATM 2 XE XE Z 2 54.986 76.636 2.746 0.11 7.49 XE > > which, to me, says that there is no binding (or at least nothing obvious). > > I finally got a good result though with 350psi and 5 minutes pressurization. After AutoSol, FOM=0.436, Bayes-CC=33.57, Model CC=0.83, Rwork/Rfree=0.2843/0.3023, 117/125 residues build and placed. And even though I told it to only look for 2 sites, Phenix went ahead and found 22 sites: > > (a, b, c, alpha, beta, gamma, space group) > CRYST1 79.130 79.130 36.920 90.00 90.00 90.00 P 43 21 2 > > (colums after numbering are a, b, c, occ, B factor) > HETATM 1 XE XE Z 1 -36.117 -56.764 -1.825 0.18 9.43 XE > HETATM 2 XE XE Z 2 -54.805 -54.805 0.000 0.14 6.44 XE > HETATM 3 XE XE Z 3 -8.337 -31.695 -16.766 0.08 8.26 XE > HETATM 4 XE XE Z 4 -5.702 -64.959 -35.134 0.05 5.21 XE > HETATM 5 XE XE Z 5 -9.535 -22.397 -31.839 0.06 14.33 XE > HETATM 6 XE XE Z 6 -7.319 -66.343 -35.123 0.05 6.02 XE > HETATM 7 XE XE Z 7 -8.580 -21.153 -30.274 0.05 7.43 XE > HETATM 8 XE XE Z 8 -1.494 -29.583 -2.339 0.06 7.36 XE > HETATM 9 XE XE Z 9 -0.518 -16.483 -16.776 0.05 6.56 XE > HETATM 10 XE XE Z 10 -0.464 -29.847 -4.386 0.06 6.04 XE > HETATM 11 XE XE Z 11 -1.222 -16.234 -18.952 0.04 6.51 XE > HETATM 12 XE XE Z 12 -6.001 -20.380 -4.532 0.05 7.22 XE > HETATM 13 XE XE Z 13 -5.169 -27.522 -10.128 0.05 3.54 XE > HETATM 14 XE XE Z 14 -11.931 -67.039 -4.699 0.05 7.96 XE > HETATM 15 XE XE Z 15 -6.538 -10.408 -3.761 0.04 10.22 XE > HETATM 16 XE XE Z 16 -0.458 -23.897 -31.221 0.05 6.85 XE > HETATM 17 XE XE Z 17 -3.308 -65.181 -8.754 0.03 8.08 XE > HETATM 18 XE XE Z 18 -11.080 -29.129 -2.144 0.04 5.61 XE > HETATM 19 XE XE Z 19 -5.720 -73.029 -2.035 0.04 11.24 XE > HETATM 20 XE XE Z 20 10.236 60.097 33.822 0.03 5.38 XE > HETATM 21 XE XE Z 21 5.980 68.581 3.532 0.03 7.49 XE > HETATM 22 XE XE Z 22 11.107 13.277 27.334 0.03 7.10 XE > > I'm pretty sure there aren't 22 sites for xenon to bind in lysozyme but it looks to me like the top 2 (maybe top 3) are actual sites which is great. > The strange part is that when I use the same data and have Phenix look for 3 or 4 sites it then only finds 3 or 4 very low occupancy sites and the CC's/R's are again all very poor. > Has anyone had this problem or does anyone know what's going on? This is the first success that I'm having with xenon derivatization and it seems to me that if Phenix can find 22 sites when asked to find 2 it should have no problem when asked to find 3 or 4. > > Thanks in advance, > ~Brennan~ ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Re: [phenixbb] Lysozyme/Xenon derivatives & Phenix.
by Terwilliger, Thomas C 02 Feb '12

02 Feb '12

Hi Brennan, The number of sites that you ask for affects the HYSS heavy-atom search procedure, but not too much else. Once some sites are found by HYSS, then autosol uses phaser to identify additional sites (that's why you got 22 sites, not 2). I am a little surprised that changing the number of sites from 2 to 4 makes the difference between finding correct sites and not finding them at all, but it does seem possible. For your experiment, one thing you could do: once you figure out where the "standard" Xe sites are, just feed them in to autosol with a sites_file=xxx.pdb for all your datasets. Then they are all starting out with pretty much the same information. All the best, Tom T ________________________________________ From: CCP4 bulletin board [CCP4BB(a)JISCMAIL.AC.UK] on behalf of Brennan Bonnet [Brennan.Bonnet(a)LIGHTSOURCE.CA] Sent: Thursday, February 02, 2012 9:43 AM To: CCP4BB(a)JISCMAIL.AC.UK Subject: [ccp4bb] Lysozyme/Xenon derivatives & Phenix. Hi all, I have a strange result using Phenix's AutoSol to look for xenon sites in lysozyme. For a few months now I have been trying to produce xenon derivatives of lysozyme using pressures in the range of 50-350psi and time ranges between 5-60min trying to find the "sweet spot" so that this technique can be applied to other proteins. For each dataset, I AutoSol using phenix and have it look for 2, 3, and 4 xenon sites. I haven't had much success though and typical values when asked to look for 2 sites have been Rwork/Rfree = 0.5585/0.5892, CC=0.14, Bayes-CC=6.5 and with xenon sites: (a, b, c, alpha, beta, gamma, space group) CRYST1 78.870 78.870 36.940 90.00 90.00 90.00 P 41 21 2 (columns after numbering are a, b, c, occ, B factor) HETATM 1 XE XE Z 1 48.601 67.475 1.088 0.06 6.58 XE HETATM 2 XE XE Z 2 54.986 76.636 2.746 0.11 7.49 XE which, to me, says that there is no binding (or at least nothing obvious). I finally got a good result though with 350psi and 5 minutes pressurization. After AutoSol, FOM=0.436, Bayes-CC=33.57, Model CC=0.83, Rwork/Rfree=0.2843/0.3023, 117/125 residues build and placed. And even though I told it to only look for 2 sites, Phenix went ahead and found 22 sites: (a, b, c, alpha, beta, gamma, space group) CRYST1 79.130 79.130 36.920 90.00 90.00 90.00 P 43 21 2 (colums after numbering are a, b, c, occ, B factor) HETATM 1 XE XE Z 1 -36.117 -56.764 -1.825 0.18 9.43 XE HETATM 2 XE XE Z 2 -54.805 -54.805 0.000 0.14 6.44 XE HETATM 3 XE XE Z 3 -8.337 -31.695 -16.766 0.08 8.26 XE HETATM 4 XE XE Z 4 -5.702 -64.959 -35.134 0.05 5.21 XE HETATM 5 XE XE Z 5 -9.535 -22.397 -31.839 0.06 14.33 XE HETATM 6 XE XE Z 6 -7.319 -66.343 -35.123 0.05 6.02 XE HETATM 7 XE XE Z 7 -8.580 -21.153 -30.274 0.05 7.43 XE HETATM 8 XE XE Z 8 -1.494 -29.583 -2.339 0.06 7.36 XE HETATM 9 XE XE Z 9 -0.518 -16.483 -16.776 0.05 6.56 XE HETATM 10 XE XE Z 10 -0.464 -29.847 -4.386 0.06 6.04 XE HETATM 11 XE XE Z 11 -1.222 -16.234 -18.952 0.04 6.51 XE HETATM 12 XE XE Z 12 -6.001 -20.380 -4.532 0.05 7.22 XE HETATM 13 XE XE Z 13 -5.169 -27.522 -10.128 0.05 3.54 XE HETATM 14 XE XE Z 14 -11.931 -67.039 -4.699 0.05 7.96 XE HETATM 15 XE XE Z 15 -6.538 -10.408 -3.761 0.04 10.22 XE HETATM 16 XE XE Z 16 -0.458 -23.897 -31.221 0.05 6.85 XE HETATM 17 XE XE Z 17 -3.308 -65.181 -8.754 0.03 8.08 XE HETATM 18 XE XE Z 18 -11.080 -29.129 -2.144 0.04 5.61 XE HETATM 19 XE XE Z 19 -5.720 -73.029 -2.035 0.04 11.24 XE HETATM 20 XE XE Z 20 10.236 60.097 33.822 0.03 5.38 XE HETATM 21 XE XE Z 21 5.980 68.581 3.532 0.03 7.49 XE HETATM 22 XE XE Z 22 11.107 13.277 27.334 0.03 7.10 XE I'm pretty sure there aren't 22 sites for xenon to bind in lysozyme but it looks to me like the top 2 (maybe top 3) are actual sites which is great. The strange part is that when I use the same data and have Phenix look for 3 or 4 sites it then only finds 3 or 4 very low occupancy sites and the CC's/R's are again all very poor. Has anyone had this problem or does anyone know what's going on? This is the first success that I'm having with xenon derivatization and it seems to me that if Phenix can find 22 sites when asked to find 2 it should have no problem when asked to find 3 or 4. Thanks in advance, ~Brennan~

2 1

Picking Rfree in thin resolution shells using command line
by Simon Kolstoe 31 Jan '12

31 Jan '12

Dear phenixbb, I see from a quick google that it is possible to pick my Rfree's using thin resolution shells (coz I've got 20 fold NCS), however as I am someone who tries to avoid the GUI where at all possible, could someone let me know what the command line way of doing this is? Thanks, Simon --------------------------------------------------------------- Dr Simon Kolstoe Laboratory for Protein Crystallography Wolfson Drug Discovery Unit University College London Rowland Hill Street, London NW3 2PF Tel: 020 7433 2765 http://www.ucl.ac.uk/~rmhasek ---------------------------------------------------------------

9 14

labelit.index python error
by Christian Roth 31 Jan '12

31 Jan '12

Hi, I had a few images, some of them are very bad. So itried to index 1 of the pictures, and indexing went very well, but then a strange error appeared which I cannot relate to anything. What might be the problem here? Best Regards Christian labelit.index_dev-968 /hosts/vulcan1/mar345/moschuetz/064c2_4/064c2_4_001.mar2300 Beam center is not immediately clear; rigorously retesting 2 solutions Beam x 172.5 y 172.9, initial score 405; refined rmsd: 0.1445 <Z>=20.4 Beam x 171.8 y 175.6, initial score 335; refined rmsd: 0.2160 <Z>=14.9 LABELIT Indexing results: Beam center x 172.58mm, y 172.91mm, distance 209.93mm ; 80% mosaicity=0.25 deg. Solution Metric fit rmsd #spots crystal_system unit_cell volume :) 2 0.2528 dg 0.105 190 monoclinic mC 248.48 71.93 154.76 90.00 112.70 90.00 2551913 :) 1 0.0000 dg 0.076 203 triclinic aP 71.93 129.30 154.76 111.69 90.25 106.07 1275944 MOSFLM Integration results: Solution SpaceGroup Beam x y distance Resolution Mosaicity RMS :) 2 C2 172.89 172.41 209.92 2.54 0.250000 0.109 1 P1 172.88 172.36 209.85 2.37 0.250000 0.094 show_stack(1): /userdata-2/christian/phenix- dev-968/labelit/command_line/screen.py(84) top_level_indexing show_stack(2): /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/../../labelit/command_line/index.py(5) <module> libc backtrace (28 frames, most recent call last): /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x8058241] /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe6) [0x4009fb56] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(main+0x17) [0x80582df] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(Py_Main+0xaba) [0x8058f2a] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(PyRun_SimpleFileExFlags+0xb5) [0x80f61fd] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(PyRun_FileExFlags+0xdc) [0x80f52cc] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(PyEval_EvalCode+0x22) [0x80d659e] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(PyEval_EvalCodeEx+0x603) [0x80d63f3] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(PyEval_EvalFrameEx+0x622e) [0x80d5ad6] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(PyEval_EvalFrameEx+0x3dc7) [0x80d366f] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(PyObject_Call+0x46) [0x806162a] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x8147760] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(PyEval_EvalCodeEx+0x4ba) [0x80d62aa] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x8145ea2] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x8064f09] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x8089ab0] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x8064f09] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x8089ab0] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x807b94a] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x80a3710] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x8089ab0] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x80a3677] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/lib/libboost_python.so [0x4036b67b] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/lib/cbflib_ext.so(boost::python::objects::value_holder<iotbx::detectors::Mar345Adaptor>::~value_holder()+0x4a) [0x42a13f22] /lib/tls/i686/cmov/libc.so.6(fclose+0x1a0) [0x400e4640] /lib/tls/i686/cmov/libc.so.6(fclose+0x41) [0x4018f241] [0x4001d400] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/lib/boost_python_meta_ext.so(boost_adaptbx_segmentation_fault_backtrace+0x1f) [0x4032231f] Segmentation fault (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319

2 1

There are still seats available for RapiData 2012, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 30 Jan '12

30 Jan '12

We are extending the deadline because seats are still available for RapiData 2012, the fourteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 22-27 April 2012: http://www.bnl.gov/rapidata/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the tenth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 22 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

1 0

Rosetta-MR - How long does it take?
by Tri Ngo 27 Jan '12

27 Jan '12

Hi Phenix users, I tried to utilize the Rosetta-MR to solve an Esterase structure (389 residues, 2 molecules/asu) which has 22% sequence identity to the know structure. I used HHPred to prepare the alignment input and Robetta fragment server to generate the fragment files. I also performed a quick test of mr-rosetta by running the command phenix_regression.wizards.test_command_line_rosetta_quick_tests. I think there is no error on my input files or the system. However, the program never finished. It still shows me the "Placing Model..." status. It's running around 48 hours and still show the same log file (at "Running group of place_model" step). I am not sure if it's normal to wait days or weeks to get the work done when running Rosetta-MR? Thank you for your helpful input. Best wishes, Tri -- * TriNgo * Structural Biology Lab School of Medicine - Sungkyunkwan University Phone: 031-299-6150 Cell: 010-7774-8210

2 1

Problems with opening Coot and Firefox from gui under RHEL 6.2
by Brick, Peter 26 Jan '12

26 Jan '12

Hi, I've installed Phenix 1.7.3-928 on a linux workstation by downloading the binary phenix-installer-1.7.3-928-intel-linux-2.6-x86_64-fc3.tar I'm running Red Hat Enterprise Linux Workstation release 6.2. (Mainly 64 bit libraries but some additional 32 bit libraries that are necessary to run Alwyn Jones' 32 bit version of O.) *Help and Firefox* When I click on the Help icon in the Phenix GUI I get the message: [pbrick@pb1 ~/test]$ phenix phenix_gui.htm Using browser /usr/bin/firefox phenix_gui.htm Using browser /usr/bin/firefox /usr/lib64/firefox-3.6/firefox: symbol lookup error: /usr/lib64/libgnome-2.so.0: undefined symbol: g_dgettext But if firefox is already running it opens a new tab and I receive no error message. Firefox is the version shipped with RHEL 6.2: firefox 3.6.24 (I notice that the mozilla website is offering version 9.0.1 for i686 processors.) *Starting Coot* When I click on the Coot icon in the Phenix gui no window opens but I can see the processes: coot, coot_build_phenix_coot.csh and coot-real running. In fact coot-real consumes 100% of the cpu of one of the cores. What I find really weird is if I look at the processes with the system monitor gui and right click and 'kill' coot-real then instead of killing the process the coot window opens. At the same time coot_build_phenix_coot.csh disappears and the cpu usage drops to zero. (Note: I've also tried the fc12 version. I found that the version of pymol distributed with phenix uses 32 bit libraries and I needed to install libXmu.so.6) Any suggestions as to what I might be doing wrong? Peter

5 6

a story of acetoacetate decarboxylase
by Kevin Jin 26 Jan '12

26 Jan '12

Dear all, I wrote a story for acetoacetate decarboxylase catalysis. I hope you will like it. http://www.jinkai.org/AAD_history.html http://www.jinkai.org/AAD_catalysis.html Regards, Kevin

1 0

Bond to symmetry mate
by Eike Schulz 26 Jan '12

26 Jan '12

Dear phenixbb, I am sure this is a trivial problem encountered before and that there is a solution to it however, I was unfortunately not able to solve it myself or with the help of the online documentation. The problem: In one of my structures a nucleic acid chain extends over several symmetry mates. How can I create and refine a bond (in my case 5'-phosphate to 3'-end ) to that symmetry mate? Many thanks in advance Eike

2 1

Twin_law in GUI Phenix Refinement
by Tri Ngo 25 Jan '12

25 Jan '12

Hi phenix users, I have two questions when using Phenix Refinement. 1. I'd like to run phenix refinement with twin data but I don't know how to define twin_law using GUI Phenix refinement module in Linux. 2. I used phenix refinement in Windows to refine a 2.3A structure. My problem is the Rfree is quite high. - I applied twin refinement + TLS + NCS and SA refinement (wxu_scale = 1) Start: r_work = 0.2149 r_free = 0.2833 bonds = 0.016 angles = 1.988 Final: r_work = 0.2029 r_free = 0.2735 bonds = 0.008 angles = 1.448 - Then I use auto-weight to optimize the Rfree. optimize_xyz_weight = True optimize_adp_weight = True wxc_scale = 0.5 wxu_scale = 1 Start: r_work = 0.2152 r_free = 0.2735 bonds = 0.008 angles = 1.322 Final: r_work = 0.2309 r_free = 0.2781 bonds = 0.003 angles = 0.848 I think the bond rmsd and angle rmsd were too small in this final refinement. Do you think it's normal or I need to try more? Thank you very much for your helpful input. Best wishes, -- * TriNgo * Structural Biology Lab School of Medicine - Sungkyunkwan University Phone: 031-299-6150 Cell: 010-7774-8210

4 4

model_vs_data
by Karolina Michalska 25 Jan '12

25 Jan '12

Hi everybody, I 've run model_vs_data for one of my structures and here is what I got: Information extracted from PDB file header: program_name : REFMAC year : None r_work : 0.15793 r_free : 0.19845 high_resolution : 1.45 low_resolution : 36.92 sigma_cutoff : None matthews_coeff : None solvent_cont : None TLS : False (number of groups: 0) After applying resolution and sigma cutoffs: n_refl_cutoff : 26357 r_work_cutoff : 0.1450 r_free_cutoff : 0.1687 Can someone, please, explain why there is such a big difference in R values? When I do refinement in phenix I get practically the same results that Refmac produces. Thanks, Karolina

3 3

links in phenix
by Christian Roth 25 Jan '12

25 Jan '12

Hi, I have a pdb with a sugar chain as ligand. I used phenix ready set to get the links according to the link remarks in the pdb. However when I look into the edits file. All links are defined as geometry restraints and despite it is alpha 1-4 all bond restraints differ slightly in their length. Within the pdb file the definitions for the links were set to alpha1-4. A Similar thing happend with a peptide link between 2 Aminoacids which have not a continously numbering because of a deletion, but it is a simple peptide bond. I modified the .link.edits file accordingly for the sugars like this ---------- refinement.geometry_restraints.edits { apply_cif_link { data_link = ALPHA1-4 atom_selection_1 = name O4 and chain B and resname GLC and resseq 1 atom_selection_2 = name C1 and chain B and resname GLC and resseq 2 } } ------------ And applied a trans link for the peptide bond I added the modified file as additional parameter file in the gui. However in the final .eff file I found just the old restraints from the previous run. In the final .eff file it is stated that the file with my updated links is loaded ------ gui { base_output_dir = "/homes/roth/structure/250/082_c2_5/refinement/phenix" tmp_dir = "/homes/roth/structure/250/082_c2_5/refinement/phenix/phenix/tmp" send_notification = False notify_email = "christian.roth(a)bbz.uni-leipzig.de" add_hydrogens = True skip_rsr = False phil_file = "/homes/roth/structure/250/082_c2_5/refinement/phenix/refmac20link.link.edits" ----- Somehow the old restraits are already in the .eff file and the new ones are ignored how I could I avoid this. Simply closing the GUI an reopening? A second question is a very non standard peptide link due to a SNN residue in the chain. Based on the link a geometry restrain is created througn phenix.link_edits There is a slight difference in the length between the N- terminal and the C-terminal peptide bond. Which is probably fine and the resoution is good enough (roughly 2 Ang.) that is looks fine, but no angle definitions for phi psi and so on are stated. What is the best way to define this two bonds correctly for the subsequent refinement? A third question is a alpha1-4 link which extend to a symmetry related sugar. How I incorporate the symmetry information into the link? A last question regarding the hydrogens in refinement. For rebuilding it is nice to remove the hydrogens. Normally I use the commandline for this purpose. But It would be nice to do it automatically after refinement as a third pdb output in addition to the two standard outputs phenix_output.pdb and the phenix_output_reduce.pdb. Is there an option in the GUI to do this automatically. I thought I have seen this previously but cannot find it anymore I am sorry for this long Mail and so many question. I hope you could help me to clarify some the things. Best Regards Christian

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DEN Refinement in phenix 1.7.3
by Eike Schulz 24 Jan '12

24 Jan '12

Dear phenixbb, I have noticed that in (since?) the latest release it is possible to activate DEN refinement in phenix.refine. I assume this refers to deformable elastic networks right? What is your experience with DEN refinements ? As I could not find any reference to it in the documentation I would be happy to have feedback on when to use and when to avoid it e.g. resolution limits etc. and what to watch out for. Many thanks in advance Eike

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