- phenixbb - phenix-online.org

Bulk solvent scaling & unstructured protein
by Mads Beich-Frandsen 24 Mar '10

24 Mar '10

Hi all, I have a P1-crystal and data (quite anisotropic to 2.85Å, 90% complete) of a partly unstructured protein, of which some 35% of the sequence is intrinsically unstructured. The structure has been solved by molecular replacement, and it has been refined to Rw/Rf 20/26 with Phenix. As expected, not much of the predicted unstructured region show clear density. The oligomeric protein packs in layers facing oneanother, leaving the unstructured parts 'packing' towards eachother, in what appears as huge solvent-channels. My question is now: Is there an approach to optimizing bulk solvent scaling in Phenix, keeping with the thought, that 30-35% of my protein sequence should be present where Phenix assigns bulk solvent. Thank you! -And any other tricks and tips will much appreciated! Rgds., Mads ------------------------------ Mads Beich-Frandsen Department of Structural and Computational Biology Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria E-mail: mads.beich-frandsen(a)univie.ac.at Phone: +43-1-4277-52225 Fax: +43-1-4277-9522 Web: http://www.mfpl.ac.at/index.php?cid=58

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where to find phenix.phaser 2.2.3 documentation on keywords
by Bjørn Panyella Pedersen 24 Mar '10

24 Mar '10

Dear list I am struggling to find the documentation for Phaser 2.2.3 (as part of phenix.phaser v1.6.289), and more specifically the list of allowed keywords and what their significance is. In my hands the PACK keyword is no longer allowed in v2.2.3 (works fine in v2.1.4) while two alternatives: SELECT CUTOFF DISTANCE and QUICK are suggested instead. However I cannot find any details on what these do. Ultimately I want to allow packing clashes beyond the default of 10. A google-search only give me hits on the Phaser homepage with documentation for v.2.1 (http://www-structmed.cimr.cam.ac.uk/phaser/documentation/index.html), and the phenix.phaser documentation (http://www.phenix-online.org/documentation/phaser.htm) does not include a keyword-list. Hope somebody can help with this simple problem. Best Bjørn -- Bjørn Panyella Pedersen, PhD Postdoc PUMPKIN, Centre for Membrane Pumps in Cells and Disease University of Aarhus, Dept. Molecular Biology Gustav Wieds Vej 10C DK-8000 Aarhus C, Denmark Phone: +45 89425261 E-mail: bjopp(a)bioxray.au.dk http://www.bioxray.au.dk

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question about autosol
by crystallogrphy 22 Mar '10

22 Mar '10

Hi, When I run phenix.autosol with this scripts (phenix.autosol data=output-anomalous.sca input_phase_file=AutoMR_run_10_/MR.1.mtz input_phase_labels="F PHIC FOM" f_prime=-8.13 f_double_prime=5.61 kp-zntb.seq atom_type=Zn), the job is terminated by the error message. Does anyone know what I should do? I am using Phenix-1.5 version. Floating-point error (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.

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help with geometry target weight
by Brown, Breann 18 Mar '10

18 Mar '10

I am currently refining a structure at 2.4A resolution. I would like to increase the geometry target weight during refinement, however when I decrease wxc_scale (to 0.25 or 0.1) there is no change in the bond deviations or R factors compared to refinement with the default wxc_scale. I noticed in the refinement logfile under XYZ refinement wc=0. This does not change when I change the wc value in the command line (wc=2.0 for example) as suggested in a previous email. I also see no change when I use the optimize_wxc=true command. Examples of the command line input and output log files are below. I am currently using version 1.6-289 and would appreciate any help in resolving this issue as it seems the geometry is not being properly weighted during refinement. Thanks, Breann Breann L. Brown Department of Molecular Pharmacology, Physiology and Biotechnology Brown University Box GE-3 Providence, RI 02912 >phenix.refine data.mtz model.pdb ligand.cif twin_law strategy=tls+individual_adp tls.params main.ncs=true wxc_scale=0.1 wc=2.0 ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.000000 wxc_scale = 0.100 wc = 0.000 | | angle between x-ray and geometry gradient vectors: None (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 11.057053 wxu_scale = 2.160 wu = 1.000 | | angle between Xray and ADP gradient vectors: 143.484 (deg) | |-----------------------------------------------------------------------------| ------------------------------------------------------------------------ stage angl bond chir dihe plan repu geom_target 0 : 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 1_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 1_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 2_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 2_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 3_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 3_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 4_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 4_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 5_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 5_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 6_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 6_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 7_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 7_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 8_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 8_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 9_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 9_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 10_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 10_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 10_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 ------------------------------------------------------------------------ Maximal deviations: stage angl bond chir dihe plan repu |grad| 0 : 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 1_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 1_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 2_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 2_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 3_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 3_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 4_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 4_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 5_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 5_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 6_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 6_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 7_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 7_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 8_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 8_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 9_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 9_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 10_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 10_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 10_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 -----Original Message----- From: phenixbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of Pavel Afonine Sent: Tuesday, February 23, 2010 1:40 PM To: PHENIX user mailing list Subject: Re: [phenixbb] weights optimization, add hydrogens Hi Ursula, > I am refining a 2.0 A structure in Phenix using mostly the graphical > interface. The maps are very good and the R factors are low > (0.208/0.173). But the geometry is not so great with bond deviations > of 0.208 and Angle deviations of 1.85. What is the best thing to do > to try to improve the geometry. Should I try to optimize the weights? the R-factors seem good indeed. Yes, Although the angle deviations seem ok to me, I'm concerned about the bond deviations... Yes, you can try two things: - increase the restraints strength by increasing the corresponding weight: from the command line: "wc=VALUE", where VALUE is a number somewhat larger than 1.0; from the GUI: Refinement settings -> All parameters -> Refinement target weights... -> Stereochemistry weight scale - Run automatic weight optimization (note, this may take a while to run): from the command line: use keyword: "optimize_wxc=true"; from the GUI: Refinement settings -> All parameters -> Refinement target weights... -> Optimize X-ray/stereochemistry weight Alternatively, you can send me your PDB and data file and I will tell you what exactly is not right and how to fix it. Pavel.

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Re: [phenixbb] phenix.simple_ncs_from_pdb output... OMAT?
by Thomas C. Terwilliger 17 Mar '10

17 Mar '10

Hi Francis, No, I don't think it is the same as OMAT format.Here is the format from phenix.simple_ncs_from_pdb (identical to the format from resolve): (Mapping molecule j onto molecule 1) (As input) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + 0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + 0.0000 Z + 0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + 0.0000 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is -28.39 18.81 -16.36 Operator # 2 New X-prime= -1.0000 X + -0.0035 Y + -0.0040 Z + -4.1335 New Y-prime= 0.0043 X + -0.1070 Y + -0.9943 Z +-21.6192 New Z-prime= 0.0031 X + -0.9943 Y + 0.1070 Z +-19.2559 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 24.44 -7.12 -39.79 would be represnted as: rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 0.0000 center_orth -28.3915 18.8125 -16.3621 rota_matrix -1.0000 -0.0035 -0.0040 rota_matrix 0.0043 -0.1070 -0.9943 rota_matrix 0.0031 -0.9943 0.1070 tran_orth -4.1335 -21.6192 -19.2559 center_orth 24.4419 -7.1171 -39.7930 This is in contrast to OMAT: O/RAVE Format OMAT r11 r21 r31 (note that the rotation matrix is r12 r22 r32 transposed with respect to CCP4 r13 r23 r33 or conventional matrix format) t1 t2 t3 where x' = r11 x + r12 y + r13 z + t1 y' = r21 x + r22 y + r23 z + t2 z' = r31 x + r32 y + r33 z + t3 I hope that helps! -Tom T >> Is the output rota_matrix (x3), and tran_orth(x1) in OMAT format? >> >> 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 >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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phenix.simple_ncs_from_pdb output... OMAT?
by Francis E Reyes 17 Mar '10

17 Mar '10

Is the output rota_matrix (x3), and tran_orth(x1) in OMAT format? 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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phenix.refine + metal ions
by Ralf W. Grosse-Kunstleve 17 Mar '10

17 Mar '10

George Phillips wrote: > I second Maia's 'request' to get proper scattering factors into Phenix > for metal ions! Metallobiochemists need love, too. Dear Metalimolbocheists, Available in phenix build 1.6.1-343 or higher. Example: HETATM 711 ZN ZN A1400 -1.928 -11.394 -27.827 1.00 17.21 ZN2+ ^^ Put the charge here To be sure it works, in the phenix.refine output, look for: Number of scattering types: 6 Type Number sf(0) Zn2+ 2 28.00 <<<<<< HERE S 13 16.00 Na 2 11.00 O 240 8.00 N 113 7.00 C 442 6.00 sf(0) = scattering factor at diffraction angle 0. Note: phenix.refine does not infer the charge from the atom name. It has to appear in the PDB charge columns 79-80 as shown above. Ralf

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program to display space group symmetry in three dimensions
by Karthik S 16 Mar '10

16 Mar '10

Hi, I was looking around for programs that display space group symmetry information and could not find any but perhaps i am lost for valuable or relevant keywords. I found two references TABLES and CRYST, but are there other alternatives that are more recent, or that can run on more common hardware? TABLES: http://scripts.iucr.org/cgi-bin/paper?S0021889887086060 CRYST: http://scripts.iucr.org/cgi-bin/paper?S0021889889007168 -- Karthik Graduate student Biophysics, U-M

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Number of atoms and average b-factors for specific chain IDs (with the option of specifying multiple chain IDs).
by Francis E Reyes 15 Mar '10

15 Mar '10

Is there anyway to get this quickly? Either by phenix util, web util, or whatever? Thanks! FR --------------------------------------------- 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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gtk error
by Rafael Counago 15 Mar '10

15 Mar '10

Dear all, I am running PHENIX on ubunut (karmic koala, 32 bits). On start up I am getting the following message: Gtk-Message: Failed to load module "canberra-gtk-module": libcanberra-gtk-module.so: cannot open shared object file: No such file or directory Any ideas how to solve this issue? Another question... is there a way to automatically search the old messages from the bb? Cheers, Rafael. -- Rafael Couñago Research Fellow Department of Biochemistry University of Otago 710 Cumberland St Dunedin, New Zealand ph: (03) 479 5148

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