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MR_Rosetta
by Heather Condurso 16 Jun '12

16 Jun '12

Hello all, I am working on a structure for which a good molecular replacement model doesn't really exist ( highest sequence similarity is 24% for a protein with completely different function and even worse for proteins with a more similar function). As I try and solve the phase with Se-Met derived protein, I thought I would try and use MR_rosetta and see what happens. I have also tried to use pyrosetta to generate better models, but the structure alignments suggest my protein to be primarily composed of beta sheets so the models from ab initio methods aren't great. I am using the GUI and have given my sca file, a sequence file, the 3 and 9 fragment files, and both the global and local alignment hhr files. I thought that phenix would use the hhr alignments to pull models directly from the pdb, but without giving a model pdb, MR_rosetta fails. So my question is how do I input the models? Should I download each of the pdbs and clean them up a bit? How many should I include? I unde! rstand the more I include the more computing time this will take. Can you give any recommendations as to other parameters to change keep the computing time down initially to identify the best model before extensive time is used? I appreciate any help you may be able to provide, Heather Condurso UF-Department of Chemistry condurso(a)ufl.edu

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alternate conformation clashes
by Timothy Springer 14 Jun '12

14 Jun '12

We have a 1.4 Å structure with two pseudo-symmetry related A and B chains that form a super b-sheet. An 8-residue loop has two quite different alternate, backbone conformations. When we refine the occupancy of these loops, they come out to 0.51 and 0.49, consistent with them being mutually incompatible (i.e., forced to be 0.50 and 0.50 in the ideal situation). Indeed, clashes would exist between the A chain A alternate and the B chain A alternate, but when these are A and B alternates, there is no clash. Since these are in separate chains, Phenix has no problem with an A and A clash. There is a second loop, non-contiguous in sequence, that also has clashes with one of these. We refine each of the two clashing loops as the A conformat ion. Since these are separate loops, Phenix does not seem to care and seems to treat the A conformation of one loop as if it is compatible with the B conformation of the other loop. This is great that Phenix is so forgiving, but my concern is that shouldn't by convention we reassign the conformations so that the A conformations are all compatible within the same monomer? Is there some formal convention on this, and will PDB ask us to reassign these? In a closely related 1.7 Å lattice, we have a single molecule per asymmetric unit, and now the relationship is between two symmetry-related molecules. The two conformations of loops are similar as in the 1.4 Å structure. Here, we have to keep the same alternate conformation name, and thus have a clash between A and A loops 1 but not A and B loops 1. Again there is a clash between A conformation of loop 1 and A conformation of loop 2, and we could make this go away by switching A and B in loop 2. I find it to be less confusing if we switch the conformation names in loop 2. What is the consensus view? Tim

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cif_as_mtz assertion error
by Eric Williams 14 Jun '12

14 Jun '12

I'm trying to run phenix.cif_as_mtz on a large number of PDB entries, and several entries give me an assertion error. The example below is from 8icz, but the error always seems to be the same. Traceback (most recent call last): File "/media/funky/phenix-1.8-1069/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/cif_as_mtz.py", line 544, in <module> run(sys.argv[1:]) File "/media/funky/phenix-1.8-1069/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/cif_as_mtz.py", line 135, in run incompatible_flags_to_work_set=command_line.options.incompatible_flags_to_work_set) File "/media/funky/phenix-1.8-1069/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/cif_as_mtz.py", line 197, in process_files r_free_flags = r_free_flags).mtz_object() File "/media/funky/phenix-1.8-1069/cctbx_project/mmtbx/utils.py", line 2001, in __init__ skip_twin_detection = True) File "/media/funky/phenix-1.8-1069/cctbx_project/mmtbx/utils.py", line 2113, in get_r_factor twin_laws = twin_laws) File "/media/funky/phenix-1.8-1069/cctbx_project/mmtbx/utils.py", line 1556, in fmodel_simple assert f_obs.sys_absent_flags().data().count(True)==0 Any ideas? Thanks. :) Eric Williams PhD candidate Intelligent Systems Program University of Pittsburgh

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run time crashing
by CPMAS Chen 14 Jun '12

14 Jun '12

It crashes during rotamer fix at the initial stage. If you like, I can send you the necessary file for you to debugging. > > Message: 7 > Date: Thu, 14 Jun 2012 08:24:44 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] phenixbb Digest, Vol 79, Issue 4 > Message-ID: <4FDA023C.3070306(a)lbl.gov> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hi, > > how long does it take to reproduce this problem in your case? So far I > have examples that take forever before they crash. So if yours takes a > few minutes I would be very interested to have it for debugging. > > Also, Jeff is going to try something else that may eliminate this problem. > > Thanks, > Pavel > > *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Re: [phenixbb] phenixbb Digest, Vol 79, Issue 4
by CPMAS Chen 14 Jun '12

14 Jun '12

I thought I am the only one have this problem. I have encountered the same problem with the newest version of phenix. My installation is on MacOS X 10.6.8. If more information needed, I am happy to provide. Traceback (most recent call last): File "/usr/local/phenix-1.8-1069/build/mac-intel-osx-x86_64/../../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-1.8-1069/phenix/phenix/refinement/command_line.py", line 146, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.8-1069/phenix/phenix/refinement/driver.py", line 1510, in run ncs_manager = self.ncs_manager) File "/usr/local/phenix-1.8-1069/phenix/phenix/refinement/strategies.py", line 575, in refinement_machine log=log) File "/usr/local/phenix-1.8-1069/cctbx_project/mmtbx/torsion_restraints/torsion_ncs.py", line 884, in fix_rotamer_outliers monitor_clashscore=False) File "/usr/local/phenix-1.8-1069/cctbx_project/mmtbx/refinement/real_space.py", line 336, in refine geometry_restraints_manager = geo_box) File "/usr/local/phenix-1.8-1069/cctbx_project/mmtbx/refinement/real_space.py", line 250, in __init__ lbfgs_exception_handling_params = lbfgs_exception_handling_params) File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 137, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/usr/local/phenix-1.8-1069/cctbx_project/scitbx/lbfgs/__init__.py", line 258, in run log) File "/usr/local/phenix-1.8-1069/cctbx_project/scitbx/lbfgs/__init__.py", line 126, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 193, in compute_functional_and_gradients compute_gradients=True) File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/manager.py", line 716, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/manager.py", line 650, in pair_proxies min_cubicle_edge=self.min_cubicle_edge) File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/__init__.py", line 1295, in __init__ shell_asu_tables=shell_asu_tables) RuntimeError: Estimated memory allocation for cubicles exceeds max_number_of_bytes: This may be due to unreasonable parameters: cubicle_edge=5 space_span=(2696.14,2555.98,2650.54) n_cubicles=(540,512,531) max_number_of_bytes=1073741824 > > Message: 1 > Date: Mon, 11 Jun 2012 11:44:07 -0700 > From: Nathaniel Echols <nechols(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] runtime error in phenix.refine > Message-ID: > <CALeAa1PBCCzKPJTMoDsFbsZMSO=SMB_19ns+mfvC3HozuUcBaQ(a)mail.gmail.com > > > Content-Type: text/plain; charset=ISO-8859-1 > > On Sun, Jun 10, 2012 at 10:04 AM, Eugene Valkov <eugene.valkov(a)gmail.com> > wrote: > > I'm encountering the following during the second macro-cycle in > > phenix.refine in latest 1.8-1069 dev build for Linux 64-bit: > > > > RuntimeError: Excessive number of cubicles: > > ?This may be due to unreasonable parameters: > > ? ?cubicle_edge=5 > > ? ?space_span=(8467.78,8440.85,8372.67) > > ? ?n_cubicles=(1694,1689,1675) > > ? ?max_number_of_bytes=101542821888 > > > > Any thoughts/suggestions much appreciated. > > If I'm interpreting the code correctly, this means that the number of > cubicles will lead to an integer format overflow - which I find hard > to believe if you're using a 64-bit system. Could you please send me > the rest of the error message, along with the output of the command > "boost_adaptbx.show_platform_info"? > > thanks, > Nat > > > -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Re: [phenixbb] phenixbb Digest, Vol 79, Issue 4
by Kay Diederichs 14 Jun '12

14 Jun '12

"A 64bit operating system" can only run on hardware that supports 64bits. Here, 64bits refers to addresses in memory - arrays larger than 4GB need 64bit addressing because 32bits do not allow high enough numbers to index such arrays. It has nothing to do with the maximum value of an integer - that is set by the programmer. A programmer can (depending on programming language and compiler) usually decide whether integer numbers should be of size 4 bytes or 8 bytes. It is just by coincidence that 8 bytes are 64 bits. Here it seems to me that a 8byte integer would be needed to hold the number of cubicles. best, Kay > Date: Mon, 11 Jun 2012 11:44:07 -0700 > From: Nathaniel Echols<nechols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] runtime error in phenix.refine > Message-ID: > <CALeAa1PBCCzKPJTMoDsFbsZMSO=SMB_19ns+mfvC3HozuUcBaQ(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Sun, Jun 10, 2012 at 10:04 AM, Eugene Valkov<eugene.valkov(a)gmail.com> wrote: >> I'm encountering the following during the second macro-cycle in >> phenix.refine in latest 1.8-1069 dev build for Linux 64-bit: >> >> RuntimeError: Excessive number of cubicles: >> ?This may be due to unreasonable parameters: >> ? ?cubicle_edge=5 >> ? ?space_span=(8467.78,8440.85,8372.67) >> ? ?n_cubicles=(1694,1689,1675) >> ? ?max_number_of_bytes=101542821888 >> >> Any thoughts/suggestions much appreciated. > > If I'm interpreting the code correctly, this means that the number of > cubicles will lead to an integer format overflow - which I find hard > to believe if you're using a 64-bit system. Could you please send me > the rest of the error message, along with the output of the command > "boost_adaptbx.show_platform_info"? > > thanks, > Nat

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MR error when fix one component and search for the other one
by fn1＠rice.edu 13 Jun '12

13 Jun '12

Hi everyone, I am trying to fix one component from the previous MR search and try to search for the other one, euler and frac are taken from the pdb file of the previous run (MR.1.pdb). Here are my input file and error message. Thanks in advance! Fengyun automr { build=false ensemble { ensembleID = "mol1" copies_to_find = 1 coords = in.pdb RMS = 0.85 } ensemble { ensembleID = "mol2" copies_to_find = 0 coords = in.pdb RMS = 0.85 } component { seq_file="mut.seq" component_type = *protein nucleic_acid component_copies = 4 } fixed_ensembles { fixed_ensembleID_list="mol2" fixed_euler_list = 206.66 146.75 96.21 fixed_frac_list = 0.688 1.011 0.005 } } i get the error message like this, ENSEMBLE: mol1 , 1 PDB file(s) ENSEMBLE: mol2 , 1 PDB file(s) Resolution set to 3.5 Specifying composition through protein sequence file /shared.scratch/ni/mut-p222-all/bb-3.5/AutoMR_run_5_/r2/mut.seq 4 Adding Ensemble mol2 as fixed solution with: Euler angles: [206.66, 146.75, 96.21] Coords (orthogonal A): [0.688, 1.011, 0.005] *************ERROR ENDING ******************* **************************************** AutoMR Input failed Python argument types in SOLU.addSOLU_6DIM_ENSE(InputMR_AUTO, str, list, bool, list, float, bool, bool, bool) did not match C++ signature: addSOLU_6DIM_ENSE(phaser::SOLU {lvalue}, std::string, scitbx::vec3<double>, bool, scitbx::vec3<double>, double, bool, bool, bool, bool, scitbx::vec3<double>, double) **************************************** *************ERROR ENDING *******************

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runtime error in phenix.refine
by Eugene Valkov 11 Jun '12

11 Jun '12

I'm encountering the following during the second macro-cycle in phenix.refine in latest 1.8-1069 dev build for Linux 64-bit: RuntimeError: Excessive number of cubicles: This may be due to unreasonable parameters: cubicle_edge=5 space_span=(8467.78,8440.85,8372.67) n_cubicles=(1694,1689,1675) max_number_of_bytes=101542821888 Any thoughts/suggestions much appreciated. Thanks, Eugene -- Dr Eugene Valkov Division of Structural Studies MRC Laboratory of Molecular Biology Hills Road, Cambridge, CB2 0QH Email: evalkov(a)mrc-lmb.cam.ac.uk Tel: +44 (0)1223 402261

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How to run normal mode analysis under command mode?
by fn1＠rice.edu 11 Jun '12

11 Jun '12

Hi everyone, I'd like to perturb my model with normal mode analysis. Does phenix have a way to do this? Thanks in advance! Fengyun

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Gordon conference - last chance!
by Anastassis Perrakis 11 Jun '12

11 Jun '12

Dear all, The registration deadline for the Gordon conference on diffraction methods in Structural Biology (15-20 July), is at the end of the week (June 17th). This is you last chance to register and get some of the places left!!! See the program and application information at: http://www.grc.org/programs.aspx?year=2012&program=diffrac Ana and Tassos

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