- phenixbb - phenix-online.org

MR_Rosetta
by Heather Condurso 15 Jun '12

15 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 10 Jun '12

10 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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Ordered solvent DOD
by YoungJin 06 Jun '12

06 Jun '12

Hi, When you add waters by ordered solvent option, is it possible putting DOD for neutron data? I added normal waters and changed them to DOD by using ReadySet. But wondering if I want to go further refinement with ordered_solvent on, how can I keep adding DOD rather than HOH. Otherwise, do I have to change again by using REadySet? I also tried to change resid name as DOD but didn't help me. Best, Young-Jin

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R/Rfree can not be reproduced
by 周文昌 03 Jun '12

03 Jun '12

Dear all, I had a weird case in which I can not reproduce the R/Rfree value for the same refinement. "same" means I run my refinement first and then I rerun with "phenix.refine *.eff --overwrite". The R/Rfree values for the two cases are different (0.2942/0.3190 vs 0.2942/0.3085). Should not they be the same always? the command I used: 1st. phenix.refine new-unique.mtz model.pdb xray_data.high_resolution=2.7 fix_rotamers=true strategy=individual_adp+individual_sites+tls ../tls_group_selections.params wxc_scale=0.05 refinement.input.xray_data.labels=FP,SIGFP --overwrite 2nd phenix.refine model_refine_001.eff --overwrite thanks, Wenchang

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Re: [phenixbb] SA omit map
by Huang, Raven H 01 Jun '12

01 Jun '12

Hi all, Was the issue of SA omit map debated last July (involving Tiaard Pining, Pavel, and Folmer) resolved in the newer version of Phenix? Specifically, We'd like to generate the same map for a ligand. It is not for the refinement, but for publication (a reviewer asked us to cover the ligand with the map in a figure). Previously, I used cns to do that (sa_omit_map.inp). But we refined our current structures solely in Phenix. If there is a choice, I'd rather not to move everything to cns and set it up just for the sake of generating a omit map. Thanks, Raven ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Raven H. Huang, Associate Professor Department of Biochemistry Center for Biophysics & Computational Biology University of Illinois at Urbana-Champaign 411 Roger Adams Lab., 600 S. Mathews Ave. Urbana, IL 61801 Phone: 217-333-3967; Fax: 217-244-5858

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partial partial occupancy
by Terry Lang 01 Jun '12

01 Jun '12

Hey Everyone, I have partially occupied ligand that I am trying model. The problem is that the ligand is in at least two conformations PLUS there is a side chain that occludes binding part of the time. In other words, I'm aiming for something like: Residue Conf A occ = 60%, Residue Conf B occ = 40%, Ligand Conf A 30%, Ligand Conf B 10%. Phenix is happy having a single conformation below 100% occupancy but seems to force the total sum of multiple occupancy residues to be 100%. Is there a way to turn that off for the ligand? Thanks Terry -- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3

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Occupancy refinement
by Jerome Nwachukwu 01 Jun '12

01 Jun '12

Hi: I have a 2.2Å structure containing a ligand in at least 2 alternate conformations. When the structure is refined via XYZ refinement + occupancy using phenix.refine, both ligand conformers are kicked out of the electron density. Is there a way to prevent this? Thank you, -Jerome Sent from my iPhone

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TLS makes my r-factors shoot through the roof
by Morten Groftehauge 30 May '12

30 May '12

Hi Phenixbb, 3.2A data, 110 Wilson B, I41, twinned. Imperfect inverted repeat dsDNA with 4 protein monomers, NCS not used in refinement. If I don't include TLS I get a nice stable R-factor while RMS goes down. If I include TLS (whether as one group per chain or as chosen by Phenix) this happens: [image: Inline images 1] Density disappears around some of the DNA bases as an obvious difference. If I run Refmac with TLS it just never finishes. While I could just refine without TLS this does make me worried that there is something wrong with my model or my data (besides being terrible). Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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Wilson B and REMARK 3
by Michael Thompson 28 May '12

28 May '12

Hello Everyone, I have a question regarding the Wilson B information reported in REMARK 3 of a pdb file. I am preparing a pdb file for deposition, and I am wondering which is the most appropriate value to report as the Wilson B in REMARK 3? My inclination is to report the Wilson B for the full dataset calculated by XSCALE. This value differs slightly from the Wilson B value calculated by phenix.refine and printed to the refinement log file (XSCALE=27.6 vs. phenix.refine=19.8). I assume this difference is due to phenix.refine using a low-resolution cutoff of ~20A. My concern stems from the fact that REMARK 3 "presents information on refinement program(s) used and the related statistics," so I'm not sure if it's best to include the Wilson B calculated by the refinement software, or the Wilson B for the whole data set. Thanks, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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Phenix crashes during refinement of a large structure
by Gino Cingolani 18 May '12

18 May '12

Hi all, PHENIX keeps crashing while refining a large structure (>18,000 residues/asym unit). Can anybody make sense of the following error message (see below)? Thanks so much, Gino ------------------------------------------------------------------------------------------------------------------------------------------------ File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model_statistics.py", line 112, in __init__ self.clashscore_obj.analyze_clashes(hierarchy = pdb_hierarchy) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/validation/clashscore.py", line 176, in analyze_clashes stdin_lines=tmp_r.as_pdb_string()) File "/usr/local/phenix-1.7.3-928/cctbx_project/libtbx/easy_run.py", line 147, in __init__ close_fds=not subprocess.mswindows) File "/usr/local/phenix-1.7.3-928/cctbx_project/libtbx/subprocess_with_fixes.py", line 598, in __init__ errread, errwrite) File "/usr/local/phenix-1.7.3-928/cctbx_project/libtbx/subprocess_with_fixes.py", line 1015, in _execute_child self.pid = os.fork() ------------------------------------------------------------------------------------------------------------------------------------------------ ****************************************************************************** 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)

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iterative-build omitmap
by ARJUN＠pitt.edu 17 May '12

17 May '12

Hi I am trying to calculate iterative-build omitmap. Initially program run all 126 omit region and created map coeffs file in corresponding TEMPO subdirectory and unable to create final combined map and this reduce program is running three days without creating the final map. I am trying to run combine_map script separately with all omit region coeffs file and I got the following error: >combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_126 combining map from binary file overall_best_denmod_map_coeffs.mtz_OMIT_REGION_126 >omit Full cross-validation will be done Setting n_small_cycle to 3 All done with inputs Building protein Setting up for building protein Standard fill-in residues: ALA A GLY G Standard main-chain atoms: N CA C O CB All main-chain atoms: N CA C O Max dist between adjacent N atoms: 6.000000 List of all residues: GLY ALA SER VAL ILE LEU MET CYS PHE TYR LYS ARG TRP HIS GLU ASP GLN ASN PRO THR List of 1-letter code of residues: GASVILMCFYKRWHEDQNPT List of number of atoms in side-chains: 0 1 2 3 4 4 4 2 7 8 5 7 10 6 5 4 5 4 3 3 checking license file.. solve2.access The date today is 17-may-12. Your license is good until 15-dec-96. >>>>>> CCP4 library signal library_file:Cannot open file (Error) raised in ccp4_file_open2 <<<<<< >>>>>> CCP4 library signal mtz:Cannot open file (Error) raised in MtzGet <<<<<< Error: failed to open file for read! Sorry, unable to open mtz file: exptl_fobs_phases_freeR_flags.mtz Sorry, unable to open mtz file resolve malloc count: 0 resolve exit_info: How to overcome this error problem Thank you P.Arjunan

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New UPDATE-- Difficult dataset and refinement--P422? I422?Twinning?
by Zhou, Tongqing (NIH/VRC) [E] 17 May '12

17 May '12

Dear All, Kay helped me reprocess the data set with XDS, the program pick up I422 as space group. It turned out that when I originally used XDS, I used spindle axis -1, 0, 0 for the APS ID22 detector, it should be 1, 0, 0. The output from XDS: SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr 8.87 4414 841 858 98.0% 2.7% 3.2% 4402 45.77 3.0% 99.9* -18 0.664 577 6.33 7883 1374 1385 99.2% 3.7% 3.9% 7872 35.76 4.1% 99.9* -17 0.687 1108 5.18 10205 1724 1734 99.4% 5.1% 4.9% 10195 29.38 5.6% 99.8* -15 0.748 1468 4.49 12194 2042 2055 99.4% 5.0% 4.7% 12185 30.77 5.4% 99.8* -20 0.727 1764 4.02 13830 2284 2297 99.4% 6.2% 5.9% 13822 24.55 6.7% 99.8* -15 0.736 2019 3.67 15377 2501 2530 98.9% 9.4% 9.3% 15368 16.77 10.3% 99.6* -12 0.752 2245 3.40 16709 2702 2724 99.2% 14.3% 14.5% 16700 11.31 15.6% 99.2* -5 0.761 2430 3.18 18091 2904 2934 99.0% 23.3% 24.6% 18084 7.14 25.4% 98.4* -3 0.726 2635 3.00 18105 2972 3107 95.7% 37.3% 40.4% 18071 4.42 40.7% 96.4* -6 0.665 2624 total 116808 19344 19624 98.6% 8.2% 8.4% 116699 18.79 9.0% 99.8* -10 0.724 16870 Attached please also find the xtriage log for data processed with XDS. Final model with I422 data set at 3 A resolution looked fine to me, r-free went down from ~0.32 to 0.298, the map even let me correctly fitted one place that supposed to have a Cis-Pro. The final numbers for the model is: r_work = 0.2611 r_free = 0.2983 bonds = 0.002 angles = 0.568 Thank you all for all the help! Regards, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4609B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ****************************************************************** -----Original Message----- From: Pavel Afonine [mailto:[email protected]] Sent: Tuesday, May 08, 2012 2:07 PM To: phenixbb(a)phenix-online.org Subject: Re: [phenixbb] UPDATE-- Difficult dataset and refinement--P422? I422?Twinning? Hi, >> 1. Is it really twinned since including twin-law in refinment gave much >> better numbers? R-factors may not be directly comparable: G.Murshudov, Appl. Comput. Math., V.10, N.2, 2011, pp.250-261. The strategy is: - check to see if Xtriage tells it's twinned (based on reflection statistics, not just predicted twin laws based on geometry); - use phenix.model_vs_data to see if it's worth using it. Pavel _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb

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annealing omit map
by r n 16 May '12

16 May '12

Hi all I have omitted some region manually from the pdb and did annealing - cartesian using phenix.refinment, the resulting map has density (1.2 sigma) in 2fofc and also seen 2.8 sigma negative density on the omitted region? any suggestions? Rab

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Re: [phenixbb] mr.rosetta gui
by Terwilliger, Thomas C 16 May '12

16 May '12

Hi Alex, OK, the problem should be fixed in tomorrow's build. Thank you for pointing it out! Let us know if that does not do it! All the best, Tom T ________________________________ From: Terwilliger, Thomas C Sent: Wednesday, May 16, 2012 10:45 AM To: PHENIX user mailing list Cc: Terwilliger, Thomas C Subject: RE: [phenixbb] mr.rosetta gui Hi Alex, Yes, I can duplicate this...I'm checking on what is happening now. All the best, Tom T ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Alexander Batyuk [batyuk(a)bioc.uzh.ch] Sent: Wednesday, May 16, 2012 1:54 AM To: PHENIX user mailing list Subject: [phenixbb] mr.rosetta gui Dear developers, While trying to run mr.rosetta from the GUI, I've encountered an error (see screenshot). I have un-checked the box Include solvation energy. The file rosetta_weights.wts has been created in WORK_1, fa_sol=0.0. Inspection of mr_rosetta_params.eff in GROUP_OF_PLACE_MODEL_1 revealed include_solvation_energy = False, followed by weights_file = "/Users/abatyuk/Desktop/o1map/MR_ROSETTA_74/WORK_1/rosetta_weights.wts", but it seems that the GUI wants either or. Is that the expected behavior? I'm running 1.8-1056, Rosetta 3.4 on OS X 10.6.8 Best wishes, Alex

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Re: [phenixbb] mr.rosetta gui
by Terwilliger, Thomas C 16 May '12

16 May '12

Hi Alex, Yes, I can duplicate this...I'm checking on what is happening now. All the best, Tom T Dear developers, While trying to run mr.rosetta from the GUI, I've encountered an error (see screenshot). I have un-checked the box Include solvation energy. The file rosetta_weights.wts has been created in WORK_1, fa_sol=0.0. Inspection of mr_rosetta_params.eff in GROUP_OF_PLACE_MODEL_1 revealed include_solvation_energy = False, followed by weights_file = "/Users/abatyuk/Desktop/o1map/MR_ROSETTA_74/WORK_1/rosetta_weights.wts", but it seems that the GUI wants either or. Is that the expected behavior? I'm running 1.8-1056, Rosetta 3.4 on OS X 10.6.8 Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun<http://www.bioc.uzh.ch/plueckthun>

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mr.rosetta gui
by Alexander Batyuk 16 May '12

16 May '12

Dear developers, While trying to run mr.rosetta from the GUI, I've encountered an error (see screenshot). I have un-checked the box Include solvation energy. The file rosetta_weights.wts has been created in WORK_1, fa_sol=0.0. Inspection of mr_rosetta_params.eff in GROUP_OF_PLACE_MODEL_1 revealed include_solvation_energy = False, followed by weights_file = "/Users/abatyuk/Desktop/o1map/MR_ROSETTA_74/WORK_1/rosetta_weights.wts", but it seems that the GUI wants either or. Is that the expected behavior? I'm running 1.8-1056, Rosetta 3.4 on OS X 10.6.8 Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

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Occupancy issue
by Simon Kolstoe 15 May '12

15 May '12

Hi phenixbb, I'm wanting to refine the occupancy for just a few Cadmium atoms in a structure but not refine any other occupancies. I've used the following command however the occupancies haven't refined: phenix.refine refinement_006.def occupancies.individual="chain X and element CD2" and the cadmiums are in the pdb file as: ATOM 8740 CD+2 CD2 X 1 -81.043 91.612 65.218 1.00 11.63 X CD2+ ATOM 8741 CD+2 CD2 X 2 -78.111 92.072 62.948 1.00 11.15 X CD2+ ATOM 8742 CD+2 CD2 X 3 -85.283 28.170 80.931 1.00 12.01 X CD2+ Thanks, Simon

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