- phenixbb - phenix-online.org

Autobuild confrusion...which files to use?
by Carl Carruthers 05 May '10

05 May '10

using the GUI, i ran AutoMR and got several files, then hit the "Run AutoBuild" button. When the AutoBuild panel came up, it automatically loaded three files from the AutoMR run: the original .mtz used in the AutoMR with Data Type as "X-ray data;" MR.mtz with Data Type as "Map Coeffs."; and MR.pdb with Data Type as "Start Model." my question is: AutoMR lists the file MR.mtz as the Data type "Phased Data." the AutoMR run also created a file named MR.MAP_coeffs.mtz with Data Type as "Map Coefficients." Why did AutoBuild load MR.mtz as the "Map Coeff" instead of the MR.MAP_coeffs.mtz file as the "Map Coeffs?" which should i use? also, thanks for a great seminar in Houston of friday. you guys are awesome.... --Carl

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anisotropy and mtz edit
by Leonid Sazanov 04 May '10

04 May '10

Hi, with highly anisotropic data we use Mark Sawaya's anistropy correction server, which works very well for electron density calculations. For refinement, we would like to use original data, but still cut to different limits over a,b,c (like 3.9 3.4 3.2 A, for example). Is there any facility for that in Phenix, and if not, can it be implemented? I know anisotropic scaling itself is done in Phaser, but would be useful also to have a possibility to cut resolution limits differently in any mtz file. -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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AUTOSOL for MAD data with error message-'Need a symfile for solve'
by Peter Czabotar 04 May '10

04 May '10

I am also having this problem, has this been corrected? I am using phenix-1.6.1 through the phenix GUI. Cheers Peter Czabotar >Hi again Frank and Graeme and Mohan, > >This is now fixed and should be available in tomorrow's build of PHENIX. >Most setting should now be available in Autosol (this bug only affected >Autosol, not Autobuild or any other PHENIX routines). > >Thanks for pointing out the problem (and Mohan if this does not solve it >in your case, please let me know and I'll continue to fix it). > >All the best, >Tom T > >> Hi Frank and Graeme and Mohan, >> >> Yes, P 2 21 21 should be allowed in autosol. I see that it doesn't work >> and I'll fix that. >> >> All the best, >> Tom T >> >> >>>> Um, this one has been hacked to death on ccp4bb: there is in fact >>>> nothing wrong or "non-standard" with that setting. If the program >>>> won't >>>> handle it, email the authors and ask them to fix it. >>>> >>>> Reindexing is an almighty pain in the butt. >>>> >>>> That said: it sounds like you may be pointing at an out-of-date >>>> symmetry operator file; I forget which environment variable it is, >>>> check the manual, but point it to an up-to-date ccp4 installation, and >>>> I >>>> suspect it will be fine. >>>> >>>> phx ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________

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B factor over 300
by Daqi Tu 04 May '10

04 May '10

Hi, I refined my structure (of which the data is very anisotropic) using phenix.refine and with individual_sites, individual_adp, and tls options turned on. From the refined coordinates, the highest B-factor in the ANISO record (ie B_tls + B_individual) is 305. This number looks rather high. Is it something I should worry about? and is there an easy way to compute the individual B-factor component? Thanks. Daqi Tu Eck lab Dana-Farber Cancer Institute

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Re: [phenixbb] Rigid body refinement question
by Ralf W. Grosse-Kunstleve 03 May '10

03 May '10

> Is it possible to specify individual residues of a chain to undergo rigid > refinement while the rest of the chain does regular refinement? No, sorry. Ralf

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nucleic acid nomencalture
by riya doreen 30 Apr '10

30 Apr '10

Hi Everyone, I am interested in refining a DNA structure with phenix. However, as soon as I read my PDB, I get a warning for missing restraints: PHENIX could not find geometry restraints in the standard monomer library for one or more residues in the PDB file" what is the correct nomenclature for DNA and RNA for use in PHENIX? Can I access phenix.elbow from the GUI ? Thanks

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NCS problems using phenix GUI on a Mac
by John Pascal 29 Apr '10

29 Apr '10

Hello, I am having difficulties defining NCS parameters using the GUI interface (Mac 10.4.11; phenix 1.6-289). Phenix will automatically select NCS restraint groups and use them during refinement. But if I edit the automated selections to my liking then click on Update and Save, the refinement runs with the original parameters unedited. I have tried reading in a ncs.param file, but it does not get read during the refinement run. Also, an intermittent problem with this GUI is that I am not allowed to "Add" a new restraint group. When I click this button, it just clears out the selections on the last group, and does not add a new group. Any ideas? Thanks. Best, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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How do I make trisaccharide, tetrasaccharides
by Hansman, Grant (NIH/VRC) [F] 29 Apr '10

29 Apr '10

How do I make trisaccharide, tetrasaccharides, etc from single monosaccharides? I.e., how do I join the monosaccharides. Do I use ideal coordinates? Can I join them in coot? I want to make HBGA Trisaccharide B. That is, I want to join FUC-GAL-GLA, it would be FUC (C1)-GAL (O2)-GAL (C2) then GAL (C3)-GAL(O3)-GLA(C1) ATOM 1 C1 FUC A 1 1.410 0.468 -0.410 1.00 10.00 C ATOM 2 C2 FUC A 1 0.120 0.513 -1.233 1.00 10.00 C ATOM 3 C3 FUC A 1 -0.831 -0.576 -0.728 1.00 10.00 C ATOM 4 C4 FUC A 1 -1.016 -0.402 0.783 1.00 10.00 C ATOM 5 C5 FUC A 1 0.359 -0.379 1.454 1.00 10.00 C ATOM 6 C6 FUC A 1 0.185 -0.241 2.967 1.00 10.00 C ATOM 7 O1 FUC A 1 2.007 -0.823 -0.535 1.00 10.00 O ATOM 8 O2 FUC A 1 0.424 0.284 -2.610 1.00 10.00 O ATOM 9 O3 FUC A 1 -2.094 -0.452 -1.385 1.00 10.00 O ATOM 10 O4 FUC A 1 -1.700 0.824 1.044 1.00 10.00 O ATOM 11 O5 FUC A 1 1.116 0.724 0.961 1.00 10.00 O ATOM 1 C1 GAL A 1 1.384 0.161 -0.445 1.00 10.00 C ATOM 2 C2 GAL A 1 0.328 -0.139 -1.512 1.00 10.00 C ATOM 3 C3 GAL A 1 -0.975 0.575 -1.139 1.00 10.00 C ATOM 4 C4 GAL A 1 -1.360 0.176 0.289 1.00 10.00 C ATOM 5 C5 GAL A 1 -0.177 0.454 1.220 1.00 10.00 C ATOM 6 C6 GAL A 1 -0.563 0.093 2.655 1.00 10.00 C ATOM 7 O1 GAL A 1 2.612 -0.476 -0.802 1.00 10.00 O ATOM 8 O2 GAL A 1 0.785 0.328 -2.782 1.00 10.00 O ATOM 9 O3 GAL A 1 -2.011 0.186 -2.044 1.00 10.00 O ATOM 10 O4 GAL A 1 -1.686 -1.213 0.327 1.00 10.00 O ATOM 11 O5 GAL A 1 0.945 -0.328 0.819 1.00 10.00 O ATOM 12 O6 GAL A 1 0.539 0.355 3.526 1.00 10.00 O ATOM 1 C1 GLA A 1 1.424 -0.489 -0.382 1.00 10.00 C ATOM 2 C2 GLA A 1 0.392 -0.498 -1.512 1.00 10.00 C ATOM 3 C3 GLA A 1 -0.650 0.592 -1.244 1.00 10.00 C ATOM 4 C4 GLA A 1 -1.222 0.387 0.163 1.00 10.00 C ATOM 5 C5 GLA A 1 -0.068 0.330 1.166 1.00 10.00 C ATOM 6 C6 GLA A 1 -0.630 0.161 2.579 1.00 10.00 C ATOM 7 O1 GLA A 1 2.043 0.797 -0.316 1.00 10.00 O ATOM 8 O2 GLA A 1 1.044 -0.242 -2.757 1.00 10.00 O ATOM 9 O3 GLA A 1 -1.700 0.498 -2.209 1.00 10.00 O ATOM 10 O4 GLA A 1 -1.958 -0.836 0.206 1.00 10.00 O ATOM 11 O5 GLA A 1 0.783 -0.771 0.859 1.00 10.00 O ATOM 12 O6 GLA A 1 0.446 0.112 3.517 1.00 10.00 O

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AutoBuild error message prime and switch
by Rebecca Oot 29 Apr '10

29 Apr '10

Hi, I'm trying to use the AutoBuild wizard to calculate a prime and switch map. When I hit run I get the following error message: The key ignore_blanks is not in var_type_dict....this means the command-line Wizard needs a conversion in the autobuild.py script under 'Translating inputs' or else in excluded_inputs. Any insight would be appreciated. Thanks Rebecca

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ReadySet for special position metal
by TC Hu 27 Apr '10

27 Apr '10

Dear all, I am refining a structure with a metal ion on a 2-fold axis, coordinated by four histidines, two from the ASU and two from symmetry. I used phenix.ready_set to generate the metal coordination file and input it into phenix.refine. However, phenix.refine complains that the customized angle restraints contain a special position atom and cannot continue. I am using Phenix 1.5.2. Could anyone suggest me how to solve this problem? Thank you! Best, Tiancen

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how to generate sharpened map for input into Pymol
by Daqi Tu 25 Apr '10

25 Apr '10

Hi, I am generating a electron density map figure in pymol for my structure. Since the data is very anisotropic, map sharpening has proven to be quite useful. The structure was solved using Phenix. How do I generate an Xplor style map in Phenix that incorporates sharpening? Thanks. Daqi Tu Postdoc Eck lab Dana-Farber Cancer Institute The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

3 3

apply_cif_link
by Hansman, Grant (NIH/VRC) [F] 24 Apr '10

24 Apr '10

I am trying to link my sugar molecule (FUC-GAL-NGA-FUC), Lewis y, for phenix.refine, but I keep on getting an error message. I am a beginner at this so I just don't know how to make the links. For , example, I am using this: refinement.pdb_interpretation { apply_cif_link { data_link = BETA1-2 residue_selection_1 = chain C and resname GAL and resid 224 residue_selection_2 = chain C and resname FUC and resid 223 } apply_cif_link { data_link = BETA1-3 residue_selection_1 = chain C and resname GAL and resid 224 residue_selection_2 = chain C and resname NGA and resid 225 } apply_cif_link { data_link = BETA1-3 residue_selection_1 = chain C and resname NGA and resid 225 residue_selection_2 = chain C and resname FUC and resid 226 Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 46 Unusual residues: {'GAL%DEL-HO2%DEL-HO3': 1, 'NGA%DEL-O1%DEL-HO3': 1, 'FUC%DEL-O1': 2} Unexpected atoms: {'NGA%DEL-O1%DEL-HO3,O1L': 1, 'NGA%DEL-O1%DEL-HO3,O': 1} Classifications: {'undetermined': 4} Modifications used: {'DEL-HO2': 1, 'DEL-HO3': 2, 'DEL-O1': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Unresolved apply_cif_link angles: 1 Unresolved apply_cif_link chiralities: 1 Number of atoms with unknown nonbonded energy type symbols: 2 "HETATM 5649 O NGA C 225 .*. O " "HETATM 5655 O1L NGA C 225 .*. O " Time building chain proxies: 2.31, per 1000 atoms: 0.41 Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 2 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary (see phenix.refine documentation). Also note that phenix.elbow is available to create restraint definitions for unknown ligands. Any help and direction would be appreciated. Grant

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Conflicting scattering type symbols: refine with TaBr
by Francis E Reyes 24 Apr '10

24 Apr '10

Hi All I'm getting an error refining with TaBr. Got tbr_exp.pdb from Hic-Up and prepared the cif with phenix.elbow. Try to do a refine with the pdb and cif and I get this error. Sorry: Conflicting scattering type symbols: initial symbol: "TA" (from pdb element column) new symbol: "T" (with residue name TBR) atom: "HETATM 1917 TA1 TBR B7131 .*. TA " What are people calling their TaBr records and/or how are they generating their cifs? Thanks F --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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can phenix.refine create a diff of the current input file with the pdb from the last run before refining?
by Francis E Reyes 23 Apr '10

23 Apr '10

Hi all, Just a feature request that phenix.refine make a diff comparing the current input file with the pdb from the last run and then doing a refinement on the input file and then allow a phenix.refine --revert to allow the user to backtrack incase the refinement isn't suitable. Right now I edit the pdb, save it as xxxx_001-input.pdb and specify xxxx_001-input.pdb as the input file in xxxx_002.def. (Yes I'm using the command line, does the GUI allow this? (i.e. right click on a refinement run then click revert?) ) F --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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negative density for heavy atom?
by Kelly Daughtry 23 Apr '10

23 Apr '10

Hello all, I have just used phenix autosol and autobuild to phase and build an initial model of my structure with phase information from Tungsten (W), collected at the peak wavelength of 1.2134 Angstroms. Autosol works beautifully! I was able to perform W-SAD and get great maps, when I initially thought I would have to perform W-MAD! The problem I am having is during phenix.refine. When I run the refinement (with and without refining the group anomalous) and including my experimental phases, I see a giant negative peak in the Fo-Fc map at the location of my Tungsten. The rest of the map is beautiful. In the log file, I can tell that the scattering factor is high for tungsten (see below). I believe the negative density is telling me I have too many electrons present at the tungsten site. Can anyone help me figure out what I am doing wrong? I have attached my latest log file. ----------X-ray scattering dictionary---------- Number of scattering types: 7 Type Number sf(0) Gaussians W 1 73.70 2 Se 1 33.92 2 S 11 15.96 2 Mg 1 11.95 2 O 462 7.97 2 N 343 6.97 2 C 1326 5.97 2 sf(0) = scattering factor at diffraction angle 0. ========================== Anomalous scatterer groups ========================= Anomalous scatterer group: Selection: "name W" Number of selected scatterers: 1 f_prime: 16.87 f_double_prime: 17.72 refine: f_double_prime Total number of atoms in anomalous groups: 1 ******************************************************* Kelly Daughtry PhD Candidate Department of Physiology and Biophysics Boston University School of Medicine 590 Commonwealth Ave R 390 Boston MA, 02215 (P) 617-358-5548 *******************************************************

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model vs Wilson b-factor
by Gino Cingolani 23 Apr '10

23 Apr '10

Hi all, we've solved a large structure (~20,000 residues/asymm unit), with 4-fold ncs and diffraction data to 3.3A. The Rfree/Rfac is ~28%-24% with OK geometry with no major outliers in the Ramachandran plot. I would think I'm done (.. after 6 years!). However, my refined model b-factor (~130A2) is >> Wilson b-factor (~80A2). Obviously I'm not too happy with it. Here is what I tried to resolve this discrepancy: --> play with wxu_scale --> play with B-factor weight in ncs restraint (4-fold ncs) --> play with number of macrocycles --> Redefine tls groups So far nothing really works, except switching from individual_adp to group_adp. However, this increases my Rfree by almost 3%. Any ideas? Thanks in advance, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

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Phaser question : MR+SAD after refinement
by Peter Grey 23 Apr '10

23 Apr '10

Dear All, I solved a structure by MR+SAD in Phaser, refined it, and would like now to let Phaser locate additional heavy atom. Should I remove the anomalous scatterers from the "PARTIAL PDB" I input to Phaser ? Thank you for your time, Peter

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Error in the end of phenix-refine with NCS
by José Trincão 23 Apr '10

23 Apr '10

Hello, I ran 2 jobs of phenix.refine with ncs (disabled automatic definition) and real-space refinement, weight optimization, 3 macrocycles. In the end of the third macrocycle I got these error messages for both: ===================== NCS restraints at end of refinement ===================== NCS restraint group 1: NCS operator 1: Reference selection: "chain A" Other selection: "chain B" Number of atom pairs: 9281 Traceback (most recent call last): File "/usr/local/phenix-1.6.1-357/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.6.1-357/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.6.1-357/phenix/phenix/refinement/driver.py", line 1187, in run out = log) File "/usr/local/phenix-1.6.1-357/cctbx_project/mmtbx/ncs/restraints.py", line 713, in show_operators ncs_operators.show(sites_cart=sites_cart, out=out, prefix=prefix+" ") File "/usr/local/phenix-1.6.1-357/cctbx_project/mmtbx/ncs/restraints.py", line 470, in show prefix=prefix+" ") File "/usr/local/phenix-1.6.1-357/cctbx_project/libtbx/utils.py", line 690, in write file_object.write(str) IOError: [Errno 5] Input/output error What could be the problem? Thanks. Jose José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal "It's very hard to make predictions... especially about the future" - Niels Bohr

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Phenix.refine in WinXP?
by Dima Klenchin 22 Apr '10

22 Apr '10

Now that Phenix has a nice GUI and all that, will there ever be a Windows version? And a similar question: has anyone managed to get phenix.refine from cci_apps for Win32 distribution running? I can't seem to make it run: 1. Installer says run \cci_apps_build\setpaths.bat The script produces an error: ******************************************* Fatal Error: Incomplete libtbx environment\! ******************************************* Please re-run the libtbx/configure.py command. 2. configure.py is found in two places: \cci_apps_sources\libtbx\configure.py \cci_apps_sources\libtbx\command_line\configure.py When I run either of them with command python configure.py I get an error "ImportError: No module named libtbx.env_config" 3. There is no file libtbx.env_config anywhere in the installation. There is file \cci_apps_build\libtbx_env. Placing it in the same directory with configure.py does not help. Even renaming libtbx_env. to libtbx.env_config and running "python configure.py" still gives an error "No module named libtbx.env_config" (?) 4. If I just run phenix.refine executable from its directory, it stops with en error: File "c:\cci_apps_sources\mmtbx\secondary_structure.py", line 941, in run_ksdssp_direct raise RuntimeError, "KSDSSP not available" RuntimeError: KSDSSP not available Thanks in advance for any help! I am comfortable setting any environmental variables manually - just need to know what they should be. Dima

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Phaser and normal mode analysis
by Francois Berenger 21 Apr '10

21 Apr '10

Hello, If I use Phaser's MR_NMA mode, will it introduce clashes into the structure or are they taken care of? Regards, Francois.

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histo-blood group antigens
by Hansman, Grant (NIH/VRC) [F] 21 Apr '10

21 Apr '10

I want to add a trisaccharide to my structure, but when I run phenix.refine the sugar breaks up. I know I need to specify the links on the sugar and that they must be in the reverse order, but I don't know how to do that. i.e., Some thing like this... which worked fine with a different sugar (below) refinement.pdb_interpretation { apply_cif_link { data_link = ALPHA1-2 residue_selection_1 = chain D and resname GAL and resid 2 residue_selection_2 = chain D and resname FUC and resid 1 } apply_cif_link { data_link = BETA1-3 residue_selection_1 = chain D and resname NGA and resid 3 residue_selection_2 = chain D and resname GAL and resid 2 BUT now I have a new sugar (below is the pdb). I want to create the links, does anyone know how to do this? HETATM 2386 C1 FUC A 1 16.834 10.319 -8.554 1.00 66.42 C HETATM 2387 C2 FUC A 1 16.606 11.012 -7.166 1.00 61.84 C HETATM 2388 C3 FUC A 1 17.009 12.513 -7.241 1.00 59.45 C HETATM 2389 C4 FUC A 1 16.144 13.200 -8.308 1.00 60.73 C HETATM 2390 C5 FUC A 1 16.343 12.478 -9.659 1.00 61.11 C HETATM 2391 C6 FUC A 1 15.451 13.074 -10.752 1.00 58.85 C HETATM 2392 O1 FUC A 1 18.293 10.173 -8.848 1.00 75.63 O HETATM 2393 O2 FUC A 1 17.360 10.357 -6.166 1.00 60.01 O HETATM 2394 O3 FUC A 1 16.815 13.162 -5.990 1.00 59.75 O HETATM 2395 O4 FUC A 1 14.774 13.159 -7.919 1.00 58.98 O HETATM 2396 O5 FUC A 1 16.051 11.063 -9.520 1.00 61.98 O HETATM 2397 C1 GAL A 2 18.717 9.760 -11.037 1.00 85.92 C HETATM 2398 C2 GAL A 2 18.373 9.162 -9.615 1.00 83.98 C HETATM 2399 C3 GAL A 2 19.592 8.289 -9.187 1.00 87.51 C HETATM 2400 C4 GAL A 2 19.814 7.192 -10.269 1.00 87.23 C HETATM 2401 C5 GAL A 2 20.123 7.872 -11.635 1.00 86.28 C HETATM 2402 C6 GAL A 2 20.336 6.876 -12.795 1.00 83.95 C HETATM 2403 O2 GAL A 2 17.629 10.430 -11.635 1.00 91.09 O HETATM 2404 O3 GAL A 2 18.638 6.383 -10.380 1.00 88.24 O HETATM 2405 O4 GAL A 2 19.031 8.744 -12.000 1.00 86.74 O HETATM 2406 O5 GAL A 2 20.641 7.401 -14.059 1.00 79.17 O HETATM 2407 O6 GAL A 2 20.370 8.579 -8.053 1.00 95.12 O HETATM 2408 C1 NGA A 3 20.960 9.184 -6.913 1.00100.54 C HETATM 2409 C2 NGA A 3 20.707 8.446 -5.548 1.00103.23 C HETATM 2410 C3 NGA A 3 20.064 9.437 -4.546 1.00103.55 C HETATM 2411 C4 NGA A 3 21.015 10.661 -4.359 1.00103.72 C HETATM 2412 C5 NGA A 3 21.252 11.342 -5.751 1.00103.24 C HETATM 2413 C6 NGA A 3 22.221 12.560 -5.693 1.00103.28 C HETATM 2414 C7 NGA A 3 20.349 6.053 -6.269 1.00107.39 C HETATM 2415 C8 NGA A 3 19.294 4.961 -6.441 1.00107.38 C HETATM 2416 N2 NGA A 3 19.860 7.256 -5.781 1.00105.47 N HETATM 2417 O3 NGA A 3 19.829 8.805 -3.291 1.00102.40 O HETATM 2418 O4 NGA A 3 22.255 10.230 -3.783 1.00105.38 O HETATM 2419 O5 NGA A 3 21.766 10.375 -6.714 1.00101.87 O HETATM 2420 O6 NGA A 3 22.993 12.697 -6.878 1.00104.86 O HETATM 2421 O7 NGA A 3 21.514 5.860 -6.552 1.00110.32 O END Kindly, Grant

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function to complete sidechains with rotamer
by Joel Bard 20 Apr '10

20 Apr '10

Hi- Is there a way in phenix to fill in missing sidechain atoms with the least clashing rotamer and set those atoms to zero occupancy? Modelers seem to prefer this to completely leaving out the atoms that aren't visible in density. Thanks, Joel

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MTZ files
by Kyle Dolan 19 Apr '10

19 Apr '10

Hi, I am trying to use the Phenix 1.3 software to solve a structure. After using AutoSol to generate initial phases from a MAD experiment at low resolution (5.0 A), I ran AutoBuild using the solve.mtz output file from AutoSol and a .sca file for higher resolution native data that I had collected from a second crystal. Since my target structure includes both protein and DNA, however, I ran several iterations of AutoBuild changing the parameters for building protein or DNA, including different models, playing with rebuild_in_place, etc. But now that I'm ready to move into manual building and refinement, I have a ton of MTZ files from my AutoBuild runs and I don't know which one(s) I should be using for my maps to guide my model-building, and which one I should consider as "the original" to use in a refinement program like phenix.refine or Refmac. Can anyone help put me on the right path? Cheers, Kyle Kyle T. Dolan Department of Biochemistry and Molecular Biology The University of Chicago ktd(a)uchicago.edu

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Fix rotamers
by Jason C Porta 17 Apr '10

17 Apr '10

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structures with problem loops / ligands
by Pavel Afonine 16 Apr '10

16 Apr '10

Hi Everyone, I'm in search of a structure that has poor or nearly no density for some relatively short loops or ligands. My search criteria are (which are flexible): - resolution 2-2.5A (slightly higher, slightly lower is ok); - structure is not large (~5000 atoms is absolute max., less is better so I can run tests quicker); - structure is nearly complete and correct - that is everything is good about the structure (almost ready-to-PDB-deposit) apart from problem loops/ligands; - no data pathologies (twinning, severe incompleteness and the likes); - length of problem loops: from 1 to 10 residues; - no restrictions on data and model use (so the structure id may appear in a future publication as an illustration, of course with all proper credits to the source); - it is desirable but not mandatory that a problem loop has some importance. Please reply to me directly. Thanks in advance! Pavel.

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Gordon Research Conference on Diffraction Methods
by A Leslie 15 Apr '10

15 Apr '10

With apologies for duplicate postings: The biannual Gordon Conference on Diffraction Methods in Structural Biology will be held at Bates College in Lewiston, Maine from 18-23rd July. The program covers all aspects of macromolecular structure solution from crystallization to structure solution and refinement and includes sessions on complementary techniques and the potential of free electron lasers. Many of the leading methods developers will be present and the format of the meeting, with free afternoons, provides ample opportunities for informal discussions. Further details, including a full program and details on the application procedure can be obtained from: http://www.grc.org/programs.aspx?year=2010&program=diffrac We hope to see you there ! Andrew Leslie (Chair) & Ana Gonzalez (Vice Chair) Outline Program: Sunday pm: Macromolecular Structures, Pushing the boundaries Discussion leader: Michael Rossmann 1. ABC Transporters: Doug Rees 2. The Spliceosome : Kyoshi Nagai Monday am: Crystallisation and the diffraction experiment Discussion leader: Zbyszek Dauter 1. Nanolitre crystallisation: Seth Harris 2. Twinning and disorder: Todd Yeates 3. Simulating the diffraction experiment: James Holton 4. Microcrystallography: Gwyndaf Evans Monday pm: Radiation damage and data collection strategies Discussion leader: Vivian Stojanoff 1. Radiation damage, experimental: Elspeth Garman 2. Microbeams: Yanhui Zou 3. Testing data collection strategies with the Pilatus: Marcus Mueller Tues am: Synchrotron developments and automated data processing Discussion leader: Thomas Schneider 1. Synchrotrons, latest developments: Sean Mc Sweeney 2. Synchrotrons, latest developments: Janet Smith 3. Data processing with Xia2/CHEF: Graeme Winter 4. Data processing with AUTOPROC: Clemens Vonrhein Tues pm: Complementary techniques Discussion leader: Ana Gonzales 1. Electron tomography: Sriram Subramaniam 2. SAXS: Hiro Tsuruta 3. Spectroscopy: Carrie Wilmot Weds am: Structure solution and refinement Discussion leader: Paul Adams 1. SAD Phasing: Randy Read 2. Molecular replacement with BALBES: Garib Murshudov 3. PHENIX: Tom Terwilliger 4. TLS: Ethan Merritt Weds pm: Challenging problems/Membrane Proteins Discussion leader: TBC 1. Using cubic lipidic phase: Martin Caffrey 2. Membrane Proteins: Stephen White 3. The Bacterial Ribosome: Venki Ramakrishnan Thurs am: Selected Posters and Map improvement and Model building Discussion leader: Tassos Perrakis 1. COOT: Paul Emsley 2. Modelling nucleic acids: Johan Hattne Thursday pm: Future Methods, FELs, Diffraction imaging Discussion leader: Ed Lattman 1. Anton Barty 2. Serial Crystallography: John Spence and Petra Fromme

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Autobuild with ligand in place?
by Claudia Scotti 15 Apr '10

15 Apr '10

Hallo! Sorry for the probably easy question. I'm trying to rebuild a model with Autobuild. The protein has a ligand, whose density is already well defined, thus that the input for the new autobuild run includes its coordinates as well. When I start the autobuild run, however, I see that the ligand is removed before rebuilding, which leads the program to use the ligand density to try to rebuild loops, thus introducing errors. How can I keep the ligand in place, please? Or is there any alternative solutions? Many thanks, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Via Ferrata, 1 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Hotmail: Free, trusted and rich email service. https://signup.live.com/signup.aspx?id=60969

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completing the description of a residue according to idealized geometry
by Peter Grey 15 Apr '10

15 Apr '10

Dear Phenix users, My crystals contains many copies of cobalt hexamine (used for SAD phasing). Currently the model contains only the cobalt ions (without the amines) and I am looking for a tool that will use the idealized geometry of cobalt hexamine to complete the description of these resdiues, i.e. add ATOM lines for the amines Is there such a tool ? Hoping, Peter

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Phenix.reflection_file_converter enhancement request
by Schubert, Carsten [PRDUS] 15 Apr '10

15 Apr '10

Hi, would it be possible to enhance the reflection file converter so that it can simultaneously write out IOBS and FOBS into the same mtz file? Right now these options seem to be mutually exclusive. The automatic conversion in phenix.refine handles that task automatically, so it should not be too hard to implement. Thanks Carsten

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Re: [phenixbb] Real Space Refinement with marginal data
by Rongjin 15 Apr '10

15 Apr '10

Hi Pavel can you show me how to select some residues that are excluded from refinement? You suggested this earlier but I did not know how to do it. I looked through the manual and I can see how to select a chain, but do not know how to select some residues. Thanks Rongjin ------------------ Original ------------------ From: "Pavel Afonine"<PAfonine(a)lbl.gov>; Date: Thu, Apr 15, 2010 08:08 AM To: "PHENIX user mailing list"<phenixbb(a)phenix-online.org>; Subject: Re: [phenixbb] Real Space Refinement with marginal data Hi Carsten, I was wondering if anyone had experience/advice for real space refinement with phenix using marginal data to 3A. I just did a run (SA, real-space refinement against diff_map, 2 fold NCS, grouped APD, fix_rotamers enabled) were the resulting structure showed lots of disconnected sidechains and some broken main chains. I am just repeating the run w/o real space refinement, may be the combination of SA and real space refinement was a bit harsh, but am wondering what kind of parameters make most sense to tweak in order to avoid having the molecules fall apart. this could be a weight issue (weight between real-space target and restraints). In general I didn't find it too beneficial doing real-space refinement globally, although I've seen cases where it made a good difference (but at higher than 3A resolution). You may try to switch to "simple" target (to make it run much faster) and turn on the weight optimization: real_space_refinement { mode = *simple diff_map target_weights = value *grid_search gradients_ratio rmsd_max_bonds = 0.05 rmsd_max_angles = 5 grid_search_scales = 0.25 0.5 0.75 1 1.25 1.5 1.75 2 2.5 3 } "fix_rotamers=true" (local real-space refinement for the residues that really need it, as determined automatically) is much better option. I thoroughly tested it up to 3A resolution and in all test cases it worked just great. Try it and see what happens for your data. Pavel.

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Real Space Refinement with marginal data
by Schubert, Carsten [PRDUS] 15 Apr '10

15 Apr '10

Hi, I was wondering if anyone had experience/advice for real space refinement with phenix using marginal data to 3A. I just did a run (SA, real-space refinement against diff_map, 2 fold NCS, grouped APD, fix_rotamers enabled) were the resulting structure showed lots of disconnected sidechains and some broken main chains. I am just repeating the run w/o real space refinement, may be the combination of SA and real space refinement was a bit harsh, but am wondering what kind of parameters make most sense to tweak in order to avoid having the molecules fall apart. Cheers Carsten

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Autobuild
by sbiswas2＠ncsu.edu 14 Apr '10

14 Apr '10

Hi all, I was wondering if you are required to delete the tmp.dat file everytime you run autobuild. What is the imporatnce of this file? I tried to run autobuild from the same folder but it did not allow me to run until I deleted this file. Thanks Shya

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xtriage and anomalous difference assessment
by Francis E Reyes 13 Apr '10

13 Apr '10

Hi all Is xtriage's assessment of anomalous signal depend on the space group chosen? (i.e. measuring genuine I+/I- or I+/I- related by symmetry operation) ? Thanks F --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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SAD Phasing
by Rajagopalan, Senapathy 13 Apr '10

13 Apr '10

Hi Everyone, I have been trying to solve a structure of a protein-DNA complex using SAD data, but am running into problems and have some questions on how phenix solves it. From Mathews coefficient calculation, I know that my protein binds to the DNA as a dimer in the asymmetric unit. And when I use this information to specify the the number of heavy atoms to look for, I always get more (1.5-2X, depending on what resolution cutoff I use) in the final heavy atom sites pdb file. More importantly, the map looks 'incomplete' in the sense that part of one of the strands in the double stranded DNA is missing. My question is if this is the result of phenix using some incorrect sites (such as with low occupancy) while phasing. If so, then how can I fix it. I have tried deleting the low occupancy sites and reading the edited heavy atom sites file explicitly using sites_file=ha.pdb, but it doesn't seem to help. Also, if I just use solve to find the heavy atom sites, those tend to be different too... Any suggestions here would be appreciated. Thanks Sena Methodist. Leading Medicine. Recognized by U.S.News & World Report as an "Honor Roll" hospital Named to FORTUNE magazine's "100 Best Companies to Work For" list five years in a row Designated as a Magnet hospital for excellence in nursing Visit us at methodisthealth.com Follow us at twitter.com/MethodistHosp and www.facebook.com/methodisthospital ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Group ADP syntax question
by Peter Grey 13 Apr '10

13 Apr '10

Hi Phenix people, Is it possible to have One B-factor per residue for one part of the structure and for other parts to use One isotropic B per selected group of atoms. For example to have one B-factor for the entire chain A and have One B-factor per each residue in chain B ? Thanks, -- Peter

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sculpt program
by sbiswas2＠ncsu.edu 12 Apr '10

12 Apr '10

Dear all, I was trying to generate a model using the sculpt program in phenix. when I run it with both alignment file and pdb file I get the following message: Processing PDB... Next model: ''... Next chain 'A'... No matching alignment for chain 'A'; delete PDB output requested Executing design... Everything is deleted; output file empty Any help with this... thanks, Shya

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assert n_ncs > 0
by Robert Ng 12 Apr '10

12 Apr '10

Hi again, How about this one ... Traceback (most recent call last): File "/usr/local/phenix-1.6.1-348/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/command_line.py", line 71, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/driver.py", line 413, in __init__ self.process_ncs_restraint_groups() File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/driver.py", line 672, in process_ncs_restraint_groups log = log) File "/usr/local/phenix-1.6.1-348/cctbx_project/mmtbx/ncs/restraints.py", line 306, in from_atom_selections log=log) File "/usr/local/phenix-1.6.1-348/cctbx_project/mmtbx/ncs/restraints.py", line 219, in __init__ assert n_ncs > 0 AssertionError Thanks again, Robert

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Optimization of the mask parameters in PHENIX
by Pascal Egea 12 Apr '10

12 Apr '10

Dear All, I am using the latest Phenix version (356) with the GUI and I would like to see the effect of optimization of the mask parameters. How can I do this with the GUI in the latest version ( I am also using the secondary structure restraints) in the manual I can see the command line phenix.refine model.pdb data.mtz optimize_mask=true however I don't see such option in the GUI (I can't see it listed in the whole list of commands) Thanks in advance -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-983-3515 lab (310)-983-3516 email pegea(a)mednet.ucla.edu

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Superimposing homologues
by Young-Jin Cho 09 Apr '10

09 Apr '10

Hi Phenix users, I am wondering if phenix or other program provide superimposing pdb files as best as possible(!) I used Superpose in CCP4 but only worked for same sequence of pdb files. So my first question is how I can superimpose more than two different pdb files that are homologues (including water or not). Of course you can do similar thing in coot or pymol, but I wonder if we have better ways to do this kind of job. Secondly, if things working, to do better superimposition, is it possible to input core domain residues information vs. flexible residues information while superimposing. Thirdly, if I have 10 different structures, is there any way to superimpose into such as a calculated average structure of them and fit others into this averaged structure for better comparison? As always, thanks in advance, Young-Jin

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fix rotamers
by Robert Ng 09 Apr '10

09 Apr '10

Dear all, I want to do fix rotamers with the phenix with my 3A resolution virus data. Just do some try out. But I got the memory error listed below: Traceback (most recent call last): File "/usr/local/phenix-1.6.1-348/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/driver.py", line 1170, in run call_back_handler = call_back_handler) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/strategies.py", line 570, in refinement_machine params = params.fit_side_chains) File "/usr/local/phenix-1.6.1-348/cctbx_project/mmtbx/refinement/fit_rotamers.py", line 779, in run map_sel = flex.abs(residual_map_data) < params.filter_residual_map_value MemoryError Does anybody has this problem before ? and know how to fix this ? Robert

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applying B_factor and scale correction to an MTZ
by Francois Berenger 09 Apr '10

09 Apr '10

Hello, Is there a tool to apply both the scale and overall B-factor correction found by the wilson plot to a given MTZ file? After applying these corrections, is there another way than redoing wilson to check that the output MTZ is on absolute scale? Thanks a lot, Francois.

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Re: [phenixbb] Superimposing homologues
by Thomas C. Terwilliger 08 Apr '10

08 Apr '10

Hi Young-Jin, phenix.superpose_pdbs fixed.pdb moving.pdb will do all these things for you except making the average structure. All the best, Tom T >> Hi Phenix users, >> I am wondering if phenix or other program provide superimposing pdb files >> as best as possible(!) >> I used Superpose in CCP4 but only worked for same sequence of pdb files. >> >> So my first question is how I can superimpose more than two different pdb >> files that are homologues (including water or not). Of course you can do >> similar thing in coot or pymol, but I wonder if we have better ways to do >> this kind of job. >> Secondly, if things working, to do better superimposition, is it possible >> to input core domain residues information vs. flexible residues >> information while superimposing. >> Thirdly, if I have 10 different structures, is there any way to >> superimpose into such as a calculated average structure of them and fit >> others into this averaged structure for better comparison? >> >> As always, thanks in advance, >> >> Young-Jin >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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OpenMP incompatible with Phenix GUI?
by Donnie Berkholz 08 Apr '10

08 Apr '10

Dear developers, I would really like to use OpenMP parallelization and also use the Phenix GUI. When I attempted a source build with OpenMP support, I was informed that the two were incompatible. My understanding is that this used to work fine with the old wizards. Would it be possible to fix this? -- Thanks, Donnie Donald S. Berkholz, Postdoctoral research fellow James R. Thompson lab, Physiology & Biomedical Engineering Grazia Isaya lab, Pediatric & Adolescent Medicine Medical Sciences 2-66 Mayo Clinic College of Medicine 200 First Street SW Rochester, MN 55905 612-991-1321

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Re: [phenixbb] phenixbb posting
by Leonid Flaks 08 Apr '10

08 Apr '10

Nathaniel Echols wrote: > The server bounced your message - are you subscribed to the list? > FYI, I'm not sure why firefox won't start here; sometimes it gets > confused by Phenix's copy of GTK, but that's not what the error > message looks like. You can try opening the Preferences in Phenix, > select the "File handling" parameters, and check "Reset > LD_LIBRARY_PATH for external apps". Let me know if that doesn't fix > the problem. > > thanks, > Nat > > ---------- Forwarded message ---------- > From: Leonid Flaks <flaks(a)bnl.gov <mailto:[email protected]>> > To: phenixbb(a)phenix-online.org <mailto:[email protected]> > Date: Wed, 07 Apr 2010 15:51:11 -0400 > Subject: problem with firefox and phenix-1.6.1-357 > I installed phenix-1.6.1-357 on Fedora-12. If I click on the question > mark in the GUI, I see the following: > > Using browser /usr/bin/firefox > /usr/lib/firefox-3.5.9/firefox: symbol lookup error: > /usr/lib/libgnome-2.so.0: undefined symbol: g_dgettext > > > and firefox would not start. I saw similar errors reported more then a > year ago, but that is a new fedora-12 installation. > > Any ideas? > > > Thanks, > > Leon > > Yes, I realized that I need to subscribe first, which I did after sending my message ;-) I tried to follow your advice - checked the box, but nothing changed. Same error message. -- Leon

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individual_sites_real_space?
by Francis E Reyes 08 Apr '10

08 Apr '10

Phenixer's I just upgraded from 1.4-87 and noticed that there's individual_sites_real_space now. The documentation (http://www.phenix-online.org/documentation/refinement.htm ) just shows that it's a parameter phenix.refine. What is this and when is it helpful (bad resolution/ bad model? or high resolution/ good model? or high resolution/bad model?) Thx F --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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LSTc refinement in phenix.refine
by JXQI 07 Apr '10

07 Apr '10

Dear all, I am refining a structure complexed with LSTc (alpha 2,6-linked galactose,i.e. SIA-GAL-NAG-GAL).I know that the BETA1-4 or BETA1-3 in the mon-lib could restrain the bond distance,but I could not find the links between the SIA and GAL......any suggestions are appreciated. Best regards Janxon

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polygon and membrane proteins
by Pascal Egea 07 Apr '10

07 Apr '10

Dear Developers, I wonder if there would be a simple way to get the Polygon program implemented in Phenix to use only membrane protein deposited structures as the reference data set. I understand that the reference set is much smaller than the whole menagerie of available structures but it represents an homogenous class of protein (crystallized in detergent). Do you think that this would be meaningful and useful? Thanks in advance, -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-983-3515 lab (310)-983-3516 email pegea(a)mednet.ucla.edu

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Re Double stranded DNA restraints?
by Thomas C. Terwilliger 07 Apr '10

07 Apr '10

Hi Sena, I would add this command helices_strands_only=True to force autobuild to just try and build helical segments. This probably won't fix the lack of connectivity however. All the best, Tom T Hi Everyone, Is there a way to force phenix (autobuild) into building a contiguous double stranded DNA. Currently, when I am solving a protein-DNA complex using SAD data: 1) its not recognizing that DNA needs to be double stranded, so it is fitting one of the strands correctly (at least part of it), but the other strand is in the protein density region. 2) It breaks down each of the strand. So it is not fitting as a contiguous 30 mer but instead a 10 mer, two 6 mers and a 8 mer. Thanks Sena

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PPC binaries?
by Marcelo Carlos Sousa 06 Apr '10

06 Apr '10

Is Phenix no longer supported on Mac PPC? ____________________________________________ Marcelo C. Sousa, Ph.D. Department of Chemistry and Biochemistry Cristol Chemistry Building. Room 100 215 UCB University of Colorado at Boulder Boulder, CO 80309 Phone: (303) 735 4341 Fax: (303) 492 5894

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(no subject)
by Prof Jennifer Martin (IMB) 04 Apr '10

04 Apr '10

The protein crystal structure I am refining has a redox modification: cysteine sulfenic acid (S-hydroxy cysteine). How do I go about including parameters for this modification in phenix refine? I have found parameters on HIC-UP (under CSO) but these are for XPLOR/ CNS. Many thanks in advance for suggestions, Jenny Martin University of Queensland

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