- phenixbb - phenix-online.org

anyone with a scalepack file with R3 or R32 using rhombohedral axes?
by Ralf W. Grosse-Kunstleve 08 Dec '10

08 Dec '10

I'm looking for a little help from the phenix user community. Does anyone have a scalepack output file with data in space group R3 or R32 using rhombohedral axes, i.e. unit cell parameters a=b=c, alpha=beta=gamma? What is the space group symbol in the file? I'm only interested to know this for files that are the direct output of scalepack. I'd like to verify that this part of the scalepack documentation is actually true: http://www.hkl-xray.com/hkl_web1/hkl/manual_online.pdf Page 139: 146 R3 R3 in hexagonal setting 446 H3 R3 in primitive setting 155 R32 R32 in hexagonal setting 455 H32 R32 in primitive setting If this is actually true, it is the exact opposite of what's used by the PDB. Thanks in advance for feedback. Ralf

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modelling of a novel protein
by intekhab alam 08 Dec '10

08 Dec '10

Hi I am trying to solve the structure of RNA polymerase in complex with its protein primer. The size of protein primer is 70 amino acids which i complexed with the polymerase and collected a data of the complex crysta at 2.3A. The space group is C2 and after Molecular replacemnet with full length polymerase in auto MR i got 3 subunits in ASU. The parameters of MR solution RFZ=71.5 TFZ=41.2 PAK=0 LLG=8812 suggests that the solution is correct. I used autobuild for model building which gave me the model of the polymerase as well as some extra density that i am considering as the other protein. After several round of refinemnt i have R and R free of 27and 32 respectively. My queries: 1. I want to know ,how can i improve my R as well as R free. 2. How can i model other protein as the density is weak and not complete, how can i improve the map of the other protein so that i can b ebale to trace the c-alpha backbone, i was able to model only 10 amino acids so far. Please guide. Regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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distorted (collapsed) zinc-finger motifs
by Hasan Demirci 07 Dec '10

07 Dec '10

Hi, I am in the middle of refining a 3.5 A (low resolution) ribonucleo-protein complex structure. Two of the proteins in this complex contain "zinc-finger" motif. These zinc-finger motifs instead of forming a cysteine-zinc interactions, cysteines are forming di or in these case tetra-sulfide bridges. Initially, zinc is centered but after refinement 4 cysteines come out collapsed and forming covalent bonds to each other and also distorted and zinc is not at the center anymore. Below is the phenix.refine zn_link.param file I am using. Many thanks for advice, Hasan Demirci ---------------------------------------------------------------------------- refinement.pdb_interpretation { disulfide_distance_cutoff = 0.1 } refinement.pdb_interpretation.apply_cif_link { data_link = ZN-CYS residue_selection_1 = chain D and resname ZN and resid 306 residue_selection_2 = chain D and resname CYS and resid 9 } refinement.pdb_interpretation.apply_cif_link { data_link = ZN-CYS residue_selection_1 = chain D and resname ZN and resid 306 residue_selection_2 = chain D and resname CYS and resid 12 } refinement.pdb_interpretation.apply_cif_link { data_link = ZN-CYS residue_selection_1 = chain D and resname ZN and resid 306 residue_selection_2 = chain D and resname CYS and resid 26 } refinement.pdb_interpretation.apply_cif_link { data_link = ZN-CYS residue_selection_1 = chain D and resname ZN and resid 306 residue_selection_2 = chain D and resname CYS and resid 31 } refinement.pdb_interpretation.apply_cif_link { data_link = ZN-CYS residue_selection_1 = chain N and resname ZN and resid 307 residue_selection_2 = chain N and resname CYS and resid 24 } refinement.pdb_interpretation.apply_cif_link { data_link = ZN-CYS residue_selection_1 = chain N and resname ZN and resid 307 residue_selection_2 = chain N and resname CYS and resid 27 } refinement.pdb_interpretation.apply_cif_link { data_link = ZN-CYS residue_selection_1 = chain N and resname ZN and resid 307 residue_selection_2 = chain N and resname CYS and resid 40 } refinement.pdb_interpretation.apply_cif_link { data_link = ZN-CYS residue_selection_1 = chain N and resname ZN and resid 307 residue_selection_2 = chain N and resname CYS and resid 43 } # data_link_ZN-CYS # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd ZN-CYS 1 ZN 2 SG single 2.340 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd ZN-CYS 1 ZN 2 SG 2 CB 109.000 3.000 ---------------------------------------------------------------------------------------------------- -- Hasan DeMirci, Ph.D. Postdoctoral Fellow Department of Molecular Biology, Cellular Biology & Biochemistry Brown University 185 Meeting Street Providence, RI 02912 (401) 863-3652 lab (SFH) (401) 863-6124 lab (ship st) (401) 226-7852 cell Hasan_DeMirci(a)Brown.edu demircha99(a)gmail.com

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Re: [phenixbb] Using Reference Structure in Phenix Refine
by John Pascal 05 Dec '10

05 Dec '10

Got it! Thank you, Pavel and Jeff. 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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Using Reference Structure in Phenix Refine
by John Pascal 05 Dec '10

05 Dec '10

Hello Everyone, I am refining against low resolution data, and I would like to use a higher resolution model that is available as a reference structure. There are multiple copies of the molecule in the asymmetric unit, each with a different chain ID. Does the reference PDB file need to contain multiple copies, such that there is a match for each chain (e.g. RESIDs and SEGIDs)? Or does phenix figure out that the reference structure refers to several copies of the molecule, and you only need a single copy in the reference molecule PDB file? Or will NCS restraints take care of this? Thanks. -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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Can PHENIX write the peak list to a PDB file?
by Joe Krahn 04 Dec '10

04 Dec '10

PHENIX has an option to find positive and negative peaks, but only lists them in the log file along with the residue they are closest to. Is it possible to write out the actual peak coordinates, such as to a PDB file? Thanks, Joe Krahn

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heavy atom search within phaser molecular replacement
by Bryan Lepore 03 Dec '10

03 Dec '10

i know that phaser will find heavy atoms in autosol, and that "MR-SAD" can be run as two separate steps, such that with some scripting, one could in principle cycle through a bunch of heavy atom searches using MR phases. however, it is not clear to me whether phaser can be run such that e.g. the refined MR solutions can have their anomalous Fourier's searched for peaks in a single MR job. seems possible in principle - before i go trying this, any comments would be appreciated.... i.e. run heavy atom searches as part of molecular replacement, for convenience. hope that makes sense. -Bryan

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Issue with phenix.superpose_maps
by Stephen Graham 03 Dec '10

03 Dec '10

Hi all, I'm trying to use phenix.superpose_maps through the GUI to get superposed maps covering the same region of NCS-related chains A and B for a figure. I have used PDB Tools to split the model into two files with only chain A or chain B. However, when I run superpose_maps specifying the two individual chains for the input PDB files but the same mtz file for the map coefficients I only get one output map (I think it overwrites the output file...). Selected input from the generated .eff file is as follows: input_files { map_1 = "/home/stepheng/blah/Native_refine_6_map_coeffs.mtz" labels_1 = 2FOFCWT,PH2FOFCWT map_2 = "/home/stepheng/blah/Native_refine_6_map_coeffs.mtz" labels_2 = 2FOFCWT,PH2FOFCWT pdb_1 = "/home/stepheng/blah/Native_refine_6_chainA.pdb" d_min_1 = None pdb_2 = "/home/stepheng/blah/Native_refine_6_chainB.pdb" d_min_2 = None output_dir = "/home/stepheng/blah" } And the end of the output is as follows: saving CCP4 map to Native_refine_6_map_coeffs_superposed.ccp4 Wrote Native_refine_6_chainA_superposed.pdb Wrote Native_refine_6_map_coeffs_superposed.ccp4 saving CCP4 map to Native_refine_6_map_coeffs_superposed.ccp4 Wrote Native_refine_6_chainB_superposed.pdb Wrote Native_refine_6_map_coeffs_superposed.ccp4 A bug? Stephen P.S. Incidentally, is there any reason you write both maps in a P1 box rather than putting map 2 on top of map 1 in the position of the first (reference) model? The latter would be more convenient as you can then re-use your carefully chosen pymol viewing matrices for all figures... -- Dr Stephen Graham 1851 Research Fellow Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital, Hills Road Cambridge, CB2 0XY, UK Phone: +44 1223 762 638

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question about xtriage
by crystallogrphy 03 Dec '10

03 Dec '10

Hi, I am checking the space group of my data set using phenix.xtriage. However, the program terminated in the following scripts. Does anyone knows why and what should I do? Thanks! phenix.xtriage B13_native.sca Traceback (most recent call last): File "/usr/local/phenix-1.6.4-486/cctbx_project/mmtbx/command_line/xtriage.py", line 20, in <module> xtriage.run(args=sys.argv[1:]) File "/usr/local/phenix-1.6.4-486/cctbx_project/mmtbx/scaling/xtriage.py", line 866, in run output_file = open( params.scaling.input.parameters.reporting.log ,'w') IOError: [Errno 13] Permission denied: 'logfile.log'

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force field of PHENIX.refine ?
by chene＠umbi.umd.edu 03 Dec '10

03 Dec '10

Dear authors of PHENIX, I just want to know what force field is used by phenix.refine, especially for simulated annealing, CHARMM, AMBER, or what else? Thanks. Chen Chen Chen, PhD, Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 240-314-6122

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distance constrain in phenix
by r n 03 Dec '10

03 Dec '10

Hi I would like to do distance restrain refinement for metal coordination. How can I do metal - protein strict distance restrain refinement in phenix? Thanks ram

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Hydrogen occupancies
by Florian Sauer 01 Dec '10

01 Dec '10

Dear all, I'm currently refining a small protein against 0.96A data using phenix.refine (1.6-486) from the GUI. Refinement without hydrogens yielded Rwork/free of 12.4/14.2. I then added H-atoms with phenix.reduce and switched to individual refinement of hydrogens which dropped the R-factors to 11.3/13.4. After this refinement the occupancies of some hydrogens dropped to 0 which makes me a little concerned. See e.g.: ATOM 752 H LYS A 45 -7.443 2.613 9.537 1.00 4.73 H ATOM 753 HA LYS A 45 -9.707 1.128 9.401 0.55 2.42 H ATOM 754 HB2 LYS A 45 -8.476 2.797 7.435 1.00 10.58 H ATOM 755 HB3 LYS A 45 -9.795 1.948 7.166 0.95 8.70 H ATOM 756 HG2 LYS A 45 -10.840 3.210 8.889 0.00 33.83 H ATOM 757 HG3 LYS A 45 -9.604 4.206 8.775 0.00 33.83 H ATOM 758 HD2 LYS A 45 -11.227 3.615 6.563 0.00 62.10 H ATOM 759 HD3 LYS A 45 -11.508 4.867 7.507 0.00 62.10 H ATOM 760 HE2 LYS A 45 -9.229 5.527 6.985 1.00 83.62 H ATOM 761 HE3 LYS A 45 -9.348 4.488 5.786 0.00 83.86 H ATOM 762 HZ1 LYS A 45 -10.909 5.758 4.853 1.00 99.63 H ATOM 763 HZ2 LYS A 45 -11.131 6.534 6.042 0.35100.44 H ATOM 764 HZ3 LYS A 45 -9.917 6.715 5.257 0.39100.08 H I would like to ask whether it is possible in phenix to group the occupancies to keep them at the same value as the rest of the residue but still refine xyz and isotropic adp of the individual hydrogens? Thank you in advance for your answers, Florian

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wander wall interaction
by subhash bihani 01 Dec '10

01 Dec '10

hi all I am working on a enzyme-ligand complex structure. For some analysis I need to remove wander wall interactions between protein and ligand. How can I do that in Phenix? Something similar to igroup statement in CNS? Thanks in adwance -- Subhash Bihani Scientific Officer Solid State Physics Division Bhabha Atomic Research Centre Trombay, Mumbai-85 Ph. 25594688 (o) alternate email: subhashbihani(a)yahoo.co.in

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phaser and threads
by Bryan Lepore 01 Dec '10

01 Dec '10

[ dev-595 ] [ GNU/Linux 2.6.31-20-generic #58-Ubuntu SMP four-processors ] [ compiled from source with --no-gui --no-apps --openmp ] i noticed phaser splits the rotation onto 2 threads - just wondering why that might be, since i used nproc=4 on the command line.... oh, hmmm... i seem to have just got this at the packing function : |python: malloc.c:4591: _int_malloc: Assertion `(unsigned long)(size) >= (unsigned long)(nb)' failed. -Bryan

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building from source : svn_checkout
by Bryan Lepore 01 Dec '10

01 Dec '10

[ dev-596 from source using --no-gui --no-apps --openmp ] README-DEV mentions ./bin/svn_checkout ... i cannot find this (but i do find bundle_update and recompile). any pointers appreciated. -Bryan

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Refinement of a complex with a symmetric inhibitor lying on the axis of symmetry
by Ina Lindemann 01 Dec '10

01 Dec '10

Hi, I try to refine a crystal structure of a protein - inhibitor complex. The protein is a homodimer and the two molecules have a crystallographic symmetry. The space group is P6122. The symmetric inhibitor binds symmetrically to the protein so that I refine the half of it. The core of the inhibitor is a five-membered ring with a nitrogen lying directly on the axis of symmetry. I achieved to refine this by setting the occupancy to 1.0. And now, here is my problem: Two C atoms of this ring system are bound across the symmetry axis - how could I include this in the refinement? Is there any possibility to generate restraints to the other part of the inhibitor (of the symmetry equivalent)?? Thanks for your help in advance, Ina Ina Lindemann Philipps-Universität Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908

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autosol : unmerged data with input_phase_file
by Bryan Lepore 30 Nov '10

30 Nov '10

dev-595 i gather that autosol will not take unmerged data when the input_phase_file originates from merged data. e.g. in "method #2 for MRSAD". -Bryan

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dev-590 compile from source : -lGLU, -lGL
by Bryan Lepore 30 Nov '10

30 Nov '10

[ dev-590 ] [ gcc 4.4.4 ] [ GNU/Linux 32-bit ] [ Ubuntu 10.10-ish ] * OpenGL/GLUT is of unstable nature* got an error compiling from source (see after sig). i tried using --openmp first, then --openmp --nogui in the same build directory and the error occurs both times. just trying this out, not critical - was interested to know if there's an easy workaround anyone might think of (besides touching GL/GLUT - shudder ). -Bryan /usr/bin/ld: cannot find -lGLU /usr/bin/ld: cannot find -lGL collect2: ld returned 1 exit status scons: *** [lib/gltbx_fonts_ext.so] Error 1

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sculptor : "Wrong alignment format:"
by Bryan Lepore 29 Nov '10

29 Nov '10

(starting a new thread?) trouble with alignment format. tried this : fubar.fas : Sorry: Unknown file(s): fubar.fas fubar.fasta : Sorry: Wrong alignment format: fubar.fasta i compared to one that worked yesterday and its not obvious : first sequence is the target, the pdb sequence is in there (somewhere), i changed a ">sp" to ">gi".... if anyone knows what i'm missing here,... -Bryan

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International Conference on Structural Genomics May 10-14, 2011, Toronto -- registration now open
by Tom Terwilliger 29 Nov '10

29 Nov '10

Dear Colleagues, We are pleased to announce that registration is now open for the International Conference on Structural Genomics 2011, which will be held in Toronto, Canada on May 10-14, 2011. This meeting is the 6th in this series of biennial meetings of the International Structural Genomics Organization. The meeting is designed to serve as a forum to discuss the most recent developments in structural genomics, structural/chemical biology, and their impact on research in biology, medicine and disease. A substantial number of short talks will be selected from submitted poster abstracts. Also, a limited number of student travel fellowships will be available for travel to this meeting. Please see http://www.icsg2011.org for further details. We hope to see you there! Best regards, Cheryl Arrowsmith ICSG 2011 Organizer Ted Baker Stephen Burley Dino Moras Joel Sussman Shigeyuki Yokoyama Tom Terwilliger ISGO Executive Committee

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occupancy refinement
by Dalibor Milic 25 Nov '10

25 Nov '10

Dear all! How to refine occupancies of mutually dependent structural fragments found in alternate conformations, but not consecutive in a sequence? E.g. I want to refine occupancies of two alternate conformations of residues 30 and 451 (see below the corresponding parts of a PDB file). Because of the nature of the structural disorder, an occupancy for altLoc A should be strictly the same in both fragments - the same is valid for altLoc B. Of course, the sum of occupancies for altLoc A and B should add up to 1. Thanks for your suggestions, Dalibor Milic ... ATOM 376 N AGLU A 30 23.241 86.975 31.961 0.52 17.13 N ATOM 377 N BGLU A 30 18.971 88.677 32.817 0.48 9.05 N ATOM 378 CA AGLU A 30 23.240 85.507 31.907 0.52 18.89 C ATOM 379 CA BGLU A 30 19.108 87.234 32.991 0.48 10.00 C ATOM 380 CB AGLU A 30 21.848 84.946 32.256 0.52 18.78 C ATOM 381 CB BGLU A 30 17.727 86.562 33.046 0.48 11.01 C ATOM 382 CG AGLU A 30 21.247 85.562 33.524 0.52 26.38 C ATOM 383 CG BGLU A 30 16.935 87.037 34.275 0.48 19.26 C ATOM 384 CD AGLU A 30 20.264 84.659 34.277 0.52 33.36 C ATOM 385 CD BGLU A 30 15.694 86.223 34.542 0.48 26.60 C ATOM 386 OE1AGLU A 30 19.437 83.968 33.620 0.52 31.85 O ATOM 387 OE1BGLU A 30 15.401 85.288 33.762 0.48 33.05 O ATOM 388 OE2AGLU A 30 20.310 84.678 35.535 0.52 29.12 O ATOM 389 OE2BGLU A 30 15.007 86.527 35.538 0.48 30.95 O ATOM 390 C AGLU A 30 23.750 84.946 30.575 0.52 18.22 C ATOM 391 C BGLU A 30 19.976 86.652 31.877 0.48 10.17 C ATOM 392 O AGLU A 30 24.319 83.853 30.534 0.52 19.40 O ATOM 393 O BGLU A 30 20.621 85.606 32.059 0.48 10.67 O ... ATOM 4627 N AALA A 451 31.047 82.837 22.335 0.52 18.30 N ATOM 4628 N BALA A 451 29.107 84.432 26.354 0.48 9.81 N ATOM 4629 CA AALA A 451 31.958 83.502 23.284 0.52 18.73 C ATOM 4630 CA BALA A 451 29.655 85.424 27.274 0.48 9.73 C ATOM 4631 CB AALA A 451 32.880 84.486 22.541 0.52 20.38 C ATOM 4632 CB BALA A 451 30.469 86.474 26.478 0.48 11.60 C ATOM 4633 C AALA A 451 31.176 84.206 24.406 0.52 18.79 C ATOM 4634 C BALA A 451 28.556 86.128 28.089 0.48 6.84 C ATOM 4635 O AALA A 451 30.019 84.593 24.197 0.52 18.25 O ATOM 4636 O BALA A 451 27.441 86.357 27.604 0.48 6.81 O ... -- Dalibor Milic, Dr. Sc. Laboratory of General and Inorganic Chemistry Department of Chemistry Faculty of Science University of Zagreb Horvatovac 102a HR-10000 Zagreb Croatia phone: +385 1 460 6377 fax: +385 1 460 6341 e-mail: dmilic(a)chem.pmf.hr

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Re: [phenixbb] occupancy refinement
by Dalibor Milic 25 Nov '10

25 Nov '10

Just an additional comment to my previous e-mail: the refined final value of occupancies in the expression occupancy(AGLU A 30) = occupancy(BGLU A 30) = occupancy(AALA A 451) = occupancy(BALA A 451) were not equal to 0.50 and I got occupancy(AGLU A 30) + occupancy(BGLU A 30) = occupancy(AALA A 451) + occupancy(BALA A 451) < 1.00. Regards, Dalibor -- Dalibor Milic Laboratory of General and Inorganic Chemistry Department of Chemistry Faculty of Science University of Zagreb Horvatovac 102a HR-10000 Zagreb Croatia phone: +385 1 460 6377 fax: +385 1 460 6341 e-mail: dmilic(a)chem.pmf.hr

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same origin
by r n 24 Nov '10

24 Nov '10

Hi all I wanted to compare the two models from two data set. I want the MR replacement in same origin to compare their them with respect to the map and model. I tried reforigin in ccp4 , it gave me some error , that I am not aware or not clear. I did tried overlay the two model and rfree is going up. Most likely different hands, so Is there any way to compare the two model and data and modify them in Phenix either reindex or shift the model origin to same in all cases. Thought phenix.xmanip could help, not seen any option to do it command line or in the GUI. I did tried def file, but phenix.xmanip params.def , it complains me that unknown file or keyword? any help will be appreciated. Thanks ram

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sculptor
by Bryan Lepore 22 Nov '10

22 Nov '10

dev-572 I am checking out sculptor, looks pretty cool, but I provided what i thought was a clustal format alignment to sculptor using --verbose, and it reports "Sorry: Wrong alignment format:" that's it. sounds like user error, but i'm not sure where to proceed next. i tried mafft and clustalw2 output for this. a sample of a bit of the top of the .aln is below. -Bryan p.s: shouldn't readseq convert it to .pir? that'd be code 14 PIR/CODATA? CLUSTAL format alignment by MAFFT L-INS-i (v6.833b) gi|16132042|ref --ANVRLQVEGLSGQLEKNVRAQLSTIESDEVTPDRRFRARVDDAIREGLKALGYYQPTI gi|157163695|re --ANVRLQVEGLSGQLEKNVRAQLSTIESDEVTPDRRFRARVDDAIREGLKALGYYQPTI

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sculptor : alternate conformations
by Bryan Lepore 22 Nov '10

22 Nov '10

dev-586 i'll probably try this anyways, but what is the advice on alternate conformations with sculptor? -Bryan

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