July 2012 - phenixbb - phenix-online.org

problems with eLBOW: RuntimeError: Bond distance > max_reasonable_bond_distance: 696.942 > 500:
by Gino Cingolani 19 Jul '12

19 Jul '12

Hi all (Nigel), I'm trying the generate restraints for a large structure that also contains 12 ANPs, 4 ADPa and a a few more ions. When i run "phenix.elbow --do-all MR.1.pdb", phenix crashes with the following... ------------------------------------------------------------------------------ electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.8 1069 - Nigel W. Moriarty (NWMoriarty(a)LBL.Gov) ------------------------------------------------------------------------------ Input format is PDB MoleculeClass : C:20 N:11 O:22 P: 5 (PDB format) 58 atoms 0 bonds 0 angles 0 dihedrals 0 rings Molecule was trimmed MoleculeClass : C:10 N: 6 O:12 P: 3 (PDB format) 31 atoms 0 bonds 0 angles 0 dihedrals 0 rings Predicted memory usage by semi-empirical method : 47Mb Timing estimates Python portion / ATP : 100% c++ optimisation cycle / ATP : 100% Hydrogens may be required to determine the correct bonding 0:05 Hydrogenise Hydrogenise Hydrogenise Hydrogenise Hydrogenise Hydrogenise H Traceback (most recent call last): File "/usr/local/phenix-1.8-1069/build/intel-linux-2.6-x86_64/../../elbow/elbow/command_line/builder.py", line 2240, in <module> run() File "/usr/local/phenix-1.8-1069/build/intel-linux-2.6-x86_64/../../elbow/elbow/command_line/builder.py", line 2038, in run molecule = builder(molecule, options) File "/usr/local/phenix-1.8-1069/build/intel-linux-2.6-x86_64/../../elbow/elbow/command_line/builder.py", line 870, in builder pre_optimise_selections=pre_optimise_selections, File "/usr/local/phenix-1.8-1069/elbow/elbow/utilities/OptimiseMixins.py", line 1009, in ExplodeAndOptimise opt_cycles=1, File "/usr/local/phenix-1.8-1069/elbow/elbow/utilities/OptimiseMixins.py", line 270, in OptimiseSelectedAtoms show_geo=show_geo, File "/usr/local/phenix-1.8-1069/elbow/elbow/utilities/OptimiseMixins.py", line 673, in OptimiseCCTBXProgression additional_restraints=additional_restraints, File "/usr/local/phenix-1.8-1069/elbow/elbow/cctbx_api/CCTBXMixins.py", line 262, in GetNewManager debug=debug, File "/usr/local/phenix-1.8-1069/elbow/elbow/cctbx_api/geometry_manager.py", line 173, in run pair_proxies = manager.pair_proxies(sites_cart=sites_cart) File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/manager.py", line 595, in pair_proxies check_bonded_distance_cutoff(sites_cart=sites_cart) File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/manager.py", line 499, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 696.942 > 500: distance: 1 - 31: 478.879 distance: 2 - 32: 603.994 distance: 5 - 33: 595.912 distance: 7 - 34: 479.110 distance: 13 - 35: 389.539 distance: 13 - 36: 559.710 distance: 14 - 37: 561.219 distance: 16 - 38: 696.942 distance: 17 - 39: 571.138 distance: 18 - 40: 497.529 distance: 19 - 41: 593.584 distance: 20 - 42: 483.447 distance: 22 - 43: 566.195 distance: 26 - 44: 561.483 distance: 26 - 45: 470.865 distance: 28 - 46: 628.947 Any clues? All nucleotides look good by eye. Thanks, 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 Website: http://www.cingolanilab.org ****************************************************************************** "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)

2 1

Collect MR solution to same ASU?
by Francis E Reyes 17 Jul '12

17 Jul '12

I remember there being a phenix cmd line utility that collects MR solutions to the same asymmetric unit. Or was I dreaming? F --------------------------------------------- Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

2 1

CCP4 6.3.0 released
by ronan.keegan＠stfc.ac.uk 16 Jul '12

16 Jul '12

Dear All, We're very pleased to announce the release of the latest version of the CCP4 Software Suite. Version 6.3.0 (Settle) is now available from the CCP4 download website: http://www.ccp4.ac.uk/download.php The release is available for Linux, Mac OSX and Windows platforms, and delivers a number of new programs, updates and features: 1. New Components and Updates: New: Aimless (Scaling and Merging, replacement for Scala) Prosmart (Generation of external restraints for Refmac) Nautilus (Automatic building of RNA/DNA) Ample (Automatic Ab initio modelling for Molecular Replacement) Dimple (Automatic difference map calculation) Zanuda (Space group checker/validator) CMapCut (Preparation of electron-density search model for MR) Comit (Composite omit maps) Gesamt (Structure aligner not using secondary structure assignments) ViewHKL (Graphical viewer for reflection data) Updated: Mosflm v7.0.9 (Data processing/reduction) iMosflm v1.0.7 (Mosflm GUI) Pointless v1.6 (Laue group determination) Refmac v5.7 (Macromolecular refinement) Phaser v2.5.1 (Molecular Replacement and Experimental Phasing) MrBump (Automatic Molecular Replacement, now includes phaser.sculptor models) Xia2 (Automated data reduction) CCP4mg v2.6.2 (CCP4 Molecular Graphics, much improved on features and stability) CCP4 Graphical User Interface: - new automation module - provides interfaces for new and updated modules - ViewHKL option for viewing reflection (mtz) files More information on updates is available from: http://www.ccp4.ac.uk/html/CHANGESinV6_3.html 2. ARP/wARP co-distribution Release 6.3.0 marks a milestone in collaboration between CCP4 and ARP/wARP teams by releasing ARP/wARP Model Building software v7.3 jointly with CCP4 Software Suite. In order to get ARP/wARP Software, academic users need only to select the appropriate package from download pages or with our new Package Manager, and type in their name and e-mail address where required. Commerical users will be required also to provide their reference number, obtainable separately from EMBL-EM. ARP/wARP 7.3 includes the following major updates and changes (on behalf of Victor Lamzin): - The protocols for the use of NCS in protein chain tracing have been improved and expanded to a wider range of resolutions. - Common ligands can now be automatically identified and fit into a specified electron density. - The algorithm for modelling partial ligands (cocktail screening) has been replaced with a new one that applies a number of sophisticated numerical features - The ARP/wARP graphics front-end, ArpNavigator, automatically assigns secondary structure and has an improved visual presentation of a static model or real time protein or ligand building. - Supported computer platforms are Mac powerpc, Mac Intel and Linux (including 32 and 64-bit versions). - The ARP/wARP installer has been considerably updated on all platforms. - Joint software release and authentication with the CCP4 is now possible. - CCP4 6.3.0 and Refmac 5.7.0029 are the recommended versions to use with ARP/wARP 7.3. 3. 64-bit precompiled packages Starting with version 6.3.0, CCP4 distributes both 32-bit and 64-bit precompiled binaries for Linux. Note that 64-bit codes will not run on 32-bit architectures, and 32-bit codes will run on 64-bit setups only if 32-bit libraries are installed (not a default for most Linuxes). THEREFORE: PLEASE MAKE SURE THAT YOU HAVE SET THE 32-bit/64-bit SWITCH ON TOP OF THE DOWNLOAD PAGES CORRECTLY BEFORE ALL! 4. "Friendly" Coot and CCP4mg distributions Coot is known to be less portable than the rest of CCP4 Program Suite. CCP4mg is more portable and requires special builds only for older Linuxes. Our new Package Manager will try to automatically choose Coot and CCP4mg bundles that are most appropriate for your system. In addition, our new download pages will offer you a range of precompiled Coot and CCP4mg packages, from where you may choose ones that work for you. 5. New distribution mechanism We hope that you will find our new Download Pages more intuitive and convenient than before. We have worked hard to improve our Windows installer, to make it working faster and smoother. On Linux and Mac platforms, we recommend using Package Manager, a small graphical application that allows you to select the desired components, and automatically download and install them on your system. Note that Package Manager features resumable downloads, which may be useful for users with slow or less reliable Internet connection. We would like to thank all of the developers who have contributed into CCP4 6.3.0, and all of those who have helped in testing it. The following publication should be used to cite the use of CCP4: M. D. Winn, C. C. Ballard, K. D. Cowtan, E. J. Dodson, P. Emsley, P. R. Evans, R. M. Keegan, E. B. Krissinel, A. G. W. Leslie, A. McCoy, S. J. McNicholas, G. N. Murshudov, N. S. Pannu, E. A. Potterton, H. R. Powell, R. J. Read, A. Vagin and K. S. Wilson (2011) Overview of the CCP4 suite and current developments, Acta Cryst D67 235-242. CCP4 is supported by the BBSRC UK through grant BB/F0202281, as well as by the number of industrial users. CCP4 6.3.0 is out now, and we hope that you will find it a helpful advance in crystallographic computing. Best wishes, CCP4 Core Team -- Scanned by iCritical.

1 0

Van der waals interaction in phenix
by subhash bihani 16 Jul '12

16 Jul '12

Hi all, In one of my structure I have to put some water molecule in alternate confimation with amino acid residues and in another case with ligand. How do I do it in Phenix. Regards -- 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

3 2

default treatment of Intensities and structure factors in phenix.refine
by Yarrow Madrona 16 Jul '12

16 Jul '12

Hi, I recently noticed from reviewing the phenix.refine log file that phenix is scaling the input intensities using the French-Wilson Method. However, I have already run Truncate in CCP4 and have structure factors in my MTZ. So it appears that Phenix.refine ignores structure factors and uses intensities regardless. The reason I am concerned is that Nat recently mentioned that the default for the sigma I cutoff is zero. However, The default in Truncate I thought was -3. If I understand correctly, the treatment in truncate allows weak reflections to be scaled and converted to structure factors. It seems that setting the I sigma cutoff to zero would cause you to loose some useable data. Currently, the sigma_fobs_rejection_criterion and sigma_ibos_rejection_criterion = None. This is the default I guess which would be 0. So my questions are: 1. Will setting: sigma_iobs_rejection_criterion = -3 result in Phenix using a sigma I cutoff of -3? 2. How do I tell phenix to use the structure factors created by Truncate? Thanks for your help. I apologize if I have some misconceptions as I am still relatively new to crystallography. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

5 7

average temperature factor
by Ursula Schulze-Gahmen 15 Jul '12

15 Jul '12

Is there an easy way to calculate average temperature factors in phenix or another program after ADP + TLS refinement in phenix? Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

6 8

output of labelit.check_pdb_symmetry
by "Weiergräber, Oliver H." 15 Jul '12

15 Jul '12

Hello, I am using labelit.check_pdb_symmetry in order to evaluate a crystal structure with sg P21 (2 copies/asu) and all angles indistinguishable from 90 degs for potential higher (i.e. orthorhombic) symmetry. Comparison of refinement statistics clearly indicates that the most likely scenario is perfect pseudomerohedral twinning of a true P21 crystal (Rfree=0.21). Accordingly, labelit.check_pdb_symmetry reports a striking discrepancy between Rsymop(Iobs) and Rsymop(Icalc): 8 % vs 31 %, i.e. there is an additional (apparent) 2-fold symmetry in the data which cannot be explained by the model. In an attempt to force a solution for comparison and visualization purposes, I have increased the r_symop_tol parameter to 0.35; the program starts to evaluate possible space groups with fTF, yielding scores (these are correlation coefficients, right?) way above 90 %. Still, in the end it reports there are no higher symmetry solutions. Why is this? Does the program check for the contrast between the best solution and the others? Changing peak_cutoff to a "discriminative" value did not help... Best regards, Oliver ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Kennen Sie schon unseren neuen Film? http://www.fz-juelich.de/film Kennen Sie schon unsere app? http://www.fz-juelich.de/app

6 9

Re: [phenixbb] phenixbb Digest, Vol 80, Issue 6
by Yuri 13 Jul '12

13 Jul '12

On Fri, 13 Jul 2012 12:13:15 -0700, phenixbb-request(a)phenix-online.org wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Re: segmented rigid body refinement (Nathaniel Echols) > 2. Re: segmented rigid body refinement (Pavel Afonine) > 3. Re: average temperature factor (David Cobessi) > 4. Re: segmented rigid body refinement (Gino Cingolani) > 5. Re: average temperature factor (Pavel Afonine) > 6. Re: output of labelit.check_pdb_symmetry (Nicholas Sauter) > 7. Re: average temperature factor (Nathaniel Echols) > > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 12 Jul 2012 09:40:41 -0700 > From: Nathaniel Echols <nechols(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] segmented rigid body refinement > Message-ID: > <CALeAa1NE=F6Quwvsm=ijGf_j-QMxwN1KqStpwiE6NJ7bmyKnsw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > On Thu, Jul 12, 2012 at 9:33 AM, Gino Cingolani < > Gino.Cingolani(a)jefferson.edu> wrote: > >> The latter....something more analytical to split individual chains >> into >> smaller groups >> (e.g. like to define tls groups). >> > > Airlie McCoy just added some functionality to do this in Phaser using > normal mode analysis. It is still somewhat experimental and in flux > (i.e. > the program name isn't even finalized), but I will email you off-list > with > details. > > -Nat >

1 0

segmented rigid body refinement
by Gino Cingolani 12 Jul '12

12 Jul '12

Hi all, I'm refining a large oligomeric structure at low res (~6A). I'd like to define groups to use for 'segmented rigid body refinement'. Is there any rational way to define 'segments'? My macromolecule is already an oligomer on its own, so, intuitively, each protomer is a segment. Thanks, 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 Website: http://www.cingolanilab.org ****************************************************************************** "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) ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Nathaniel Echols [nechols(a)lbl.gov] Sent: Thursday, July 12, 2012 7:44 AM To: PHENIX user mailing list Subject: Re: [phenixbb] RFZ is higher than TFZ On Thu, Jul 12, 2012 at 12:38 AM, 周文昌 <wenchangyu2006(a)gmail.com> wrote: > I had one problem using phaser-MR to solve my structure. Phaser-MR gives me > one solution with TFZ=15.4 and LLG=165 which seems to be promising but > phenix.refine does not give me a low R values (0.4884/0.5424). I went back > and checked the solution from phaser-MR, I found RFZ=18.8, higher than TFZ. > Does anyone think this is a problem to solve my structure? > > The space group is C121, I believe there are 4 copies of my search model in > ASU. What is the resolution, and what is the sequence identity of the search model? I don't know whether the high RFZ means anything, but the first thing I would check is whether the packing of the MR solution makes sense; Phaser will do a good job preventing molecules from overlapping (unless you changed it to use much less conservative criteria), but it won't guarantee that the molecules pack into a nice continuous lattice. If there are big gaps, it may not be a real solution. I think we need to add an entire FAQ page for high R-factors. However, there are an increasing number of tools and/or tricks in Phenix to deal with problems like this - in approximate order of runtime: - run phenix.refine for more cycles - at least 20. See this paper for an example of why this can be important: http://journals.iucr.org/d/issues/2012/07/00/kw5044/index.html - use phenix.morph_model (refer to previously mentioned paper) - use phenix.den_refine (or DEN in CNS) - use MR-Rosetta Also, if you're willing to share your data with us, we're collecting difficult-to-refine structures for benchmarking new methods. (It will of course be kept confidential.) -Nat _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

3 5

v1.8 bug ? memory allocation crash in map calculation (phenix.refine, phenix.maps)
by Phil Jeffrey 12 Jul '12

12 Jul '12

This is in F432 in a=b=c=340A at 2.85A resolution. Mac OSX 10.5.8, the machine has 8Gb memory of which something like 6Gb is hanging around begging to be used. 1,327,104,000 if that's in bytes doesn't seem all that excessive. On the other hand, 340*340*340= 39,419,600 so it's perhaps a little greedy. Limits set by shell: phil% limit cputime unlimited filesize unlimited datasize unlimited stacksize 65532 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 266 phenix.refine does the same thing right at the end, which is kind of a shame since it takes quite a long time to run. phenix.maps does the same thing even if I ask it just to generate F,phase in MTZ format. [snip] Compute maps. Python(632) malloc: *** mmap(size=1327104000) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug show_stack(1): /usr/local/phenix-1.8-1069/cctbx_project/cctbx/miller/__init__.py(3067) double_step_filtration show_stack(2): /usr/local/phenix-1.8-1069/cctbx_project/mmtbx/maps/__init__.py(416) map_coefficients_from_fmodel show_stack(3): /usr/local/phenix-1.8-1069/cctbx_project/mmtbx/maps/__init__.py(543) __init__ show_stack(4): /usr/local/phenix-1.8-1069/build/mac-intel-osx/../../cctbx_project/mmtbx/command_line/maps.py(325) run show_stack(5): /usr/local/phenix-1.8-1069/build/mac-intel-osx/../../cctbx_project/mmtbx/command_line/maps.py(402) <module> Bus error (Python call stack 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.

3 8