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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

6 11

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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Ordered solvent DOD
by YoungJin 07 Jun '12

07 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 02 Jun '12

02 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 02 Jun '12

02 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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Refinement error with Se labeled DNA cif seting
by Lauren 15 May '12

15 May '12

Dear all, I have a protein complex with 10mer DNA with one adenine labeled with Se-CH3 at C2'. I gave the se labeled pdb structure to the Elbow or ReadySet, the program gave me the cif as shown below. When I tried to refine the structure, phenix.refine ends with a Error message: Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unexpected atoms: {'AMS,OP1': 1, 'AMS,OP2': 1} Classifications: {'DNA': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Number of atoms with unknown nonbonded energy type symbols: 2 "HETATM 2 OP1 AMS A 1 .*.A O " "HETATM 3 OP2 AMS A 1 .*.A O " Any advice on how to modified the cif or pdb files? Thanks so much in advance. CIF files: AMS P P P . 10.3639 38.8090 53.6083 AMS OP1 O OH1 . 9.8621 39.4308 52.7650 AMS OP2 O O . 9.6270 38.9790 55.3430 AMS O5' O O2 . 11.5188 37.6926 53.7178 AMS C5' C CH2 . 12.2621 37.6244 54.8065 AMS C4' C CR15 . 13.5128 36.9044 54.7141 AMS O4' O O . 14.2653 37.1385 55.8584 AMS C3' C CR15 . 13.2442 35.4155 54.6698 AMS O3' O OH1 . 14.1003 34.8289 53.7923 AMS C2' C CR15 . 13.5010 34.9324 55.9516 AMS SE2' SE SE . 11.8697 34.2402 56.7089 AMS C1' C CR15 . 13.9654 36.1199 56.7679 AMS CA' C CH3 . 11.5566 32.3937 56.0481 AMS N9 N NR5 . 15.1526 35.8937 57.6065 AMS C8 C CR15 . 16.4077 35.6661 57.1789 AMS N7 N N . 17.1943 35.5119 58.2703 AMS C5 C CR56 . 16.4320 35.6429 59.3887 AMS C4 C CR56 . 15.1196 35.8884 58.9705 AMS N1 N N . 15.6651 35.7647 61.7193 AMS C2 C CR16 . 14.4119 35.9994 61.2874 AMS N3 N N . 14.1134 36.0657 59.9478 AMS C6 C CR6 . 16.7122 35.5796 60.8007 AMS N6 N NH2 . 18.1110 35.3174 61.2840 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd AMS P OP1 single 1.162 0.02 AMS P OP2 double 1.892 0.02 AMS P O5' single 1.610 0.02 AMS O5' C5' single 1.320 0.02 AMS C5' C4' single 1.446 0.02 AMS C4' O4' single 1.389 0.02 AMS C4' C3' single 1.514 0.02 AMS O4' C1' single 1.398 0.02 AMS C3' O3' single 1.359 0.02 AMS C3' C2' single 1.394 0.02 AMS C2' SE2' single 1.927 0.02 AMS C2' C1' single 1.514 0.02 AMS SE2' CA' single 1.986 0.02 AMS C1' N9 single 1.471 0.02 AMS N9 C8 aromatic 1.345 0.02 AMS N9 C4 aromatic 1.364 0.02 AMS C8 N7 aromatic 1.354 0.02 AMS N7 C5 aromatic 1.360 0.02 AMS C5 C4 aromatic 1.399 0.02 AMS C5 C6 aromatic 1.441 0.02 AMS C4 N3 aromatic 1.414 0.02 AMS N1 C2 aromatic 1.346 0.02 AMS N1 C6 aromatic 1.405 0.02 AMS C2 N3 aromatic 1.374 0.02 AMS C6 N6 single 1.503 0.02 Best Regards Lauren

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refinement of peptide with non-standard aminocids
by Vitali Stanevich 15 May '12

15 May '12

Hi, I am trying to refine protein structure with MCLR ligand - this is cyclic hepta-peptide which has some non-standard amino acids. Sequence is DAL-LEU-ACB-ARG-1ZN-FGA-DAM. It's exactly the same compound as chain G at 3dw8 PDB entry. I could successfully import amino acids in coot through "get monomer" option, renumber and combine in one chain. Problem is that whenever I use phenix.refine it returns all residues nonbonded. Corresponding carboxyl and amino groups are in close proximity to make a bond. I tried to write LINKR record in .pdb - with no success: ... LINKR 1ZN G 5 FGA G 6 trans LINKR FGA G 6 DAM G 7 trans ... Is there a way to create peptide bonds in this inhibitor chain? I'm using phenix Version: 1.7.3. Thanks in advance, Vitali

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discrepancy in MolProbity statistics
by Michael Thompson 15 May '12

15 May '12

Hello All, I recently ran into a discrepancy between the MolProbity statistics reported by phenix.refine and the MolProbity statistics reported by the actual MolProbity webserver. I was hoping someone could comment on this and let me know if this is a warning sign that something is amiss. The structure (resolution=2.0A) seems to be correct and well refined, based on R-factors (0.1591/0.1774) and geometry reports from the various validation tools. Remark 3, which was written out to the pdb file by phenix.refine, contains the following: REMARK 3 MOLPROBITY STATISTICS. REMARK 3 ALL-ATOM CLASHSCORE : 4.14 REMARK 3 RAMACHANDRAN PLOT: REMARK 3 OUTLIERS : 0.00 % REMARK 3 ALLOWED : 2.32 % REMARK 3 FAVORED : 97.68 % REMARK 3 ROTAMER OUTLIERS : 1.83 % REMARK 3 CBETA DEVIATIONS : 0 Remark 40, which was created by and downloaded from the MolProbity web server, contains slightly different statistics: REMARK 40 MOLPROBITY OUTPUT SCORES: REMARK 40 ALL-ATOM CLASHSCORE : 0.83 REMARK 40 BAD ROTAMERS : 1.6% 8/510 (TARGET 0-1%) REMARK 40 RAMACHANDRAN OUTLIERS : 0.0% 0/657 (TARGET 0.2%) REMARK 40 RAMACHANDRAN FAVORED : 97.7% 642/657 (TARGET 98.0%) I am mainly concerned about the values of the ALL-ATOM CLASHSCORE, as they are significantly different according to the two calculations. Thanks in advance for any information/answers! 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.model
by r n 14 May '12

14 May '12

Hi I did get different values in phenix.model_vs_data, after the refinement gave me R and Rfree as 24 and 29% and phenix.model_vs_data gave me R_compute and Rfree-compute as 22 and 26%. Thought that both R-compute and refinement values should be more or less same? any suggestions R

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CASP 10: Call for targets to assess the state of the art in protein structure modeling
by Torsten Schwede 11 May '12

11 May '12

*CASP 10: Call for targets to assess the state of the art in protein structure modeling* As many of you know, CASP (Critical Assessment of Structure prediction) has been assessing the state of the art in modeling protein structure from sequence since 1994, running a community experiment once every two years. In these experiments, information on soon to be solved structures is collected from the experimental community, and the sequence data are passed to the structure modeling community so that blind predictions of structure and can collected and assessed (1). Over that period CASP has seen enormous progress in the quality of modeled structures (2), but many problems remain. CASP is only possible because of the generous participation of the experimental community in providing the modeling targets (3). We recently appealed for your help in providing novel fold and membrane protein targets for the ongoing CASP ROLL process. That is very successful, with 57 prediction teams participating and 26 targets already released, thanks to all of you who have contributed. The prediction season for the next full biannual experiment, CASP 10, begins May 1, and so we are now asking for your help again, this time in reaching our goal of releasing at least varied 100 targets in a the three-month period. We need all sorts of targets, spanning the categories below: 1. (More than ever) novel folds and membrane protein targets -- even with the extended collection season provided by CASP ROLL, there will be still a shortage. There are some interesting methods developments for ab initio modeling, and it is important to be able to decisively evaluate their effectiveness. 2. A diversity of comparative modeling targets. Cases where the there is fairly high sequence identity (30-50%) between the target structure and an available template are valuable for testing the degree to which model accuracy can approach that of experiment, particularly in functionally critical regions. Cases with lower sequence identity to template, right down to undetectable, are valuable for testing the ability of the methods to detect remote homologs, to overcome challenging alignment difficulties, to make use of multiple templates, and to build regions of the structure not obviously available from a template. 3. Targets containing significant amounts of disordered structure, so as to test the ability of methods to identify these regions. Disorder identified by absence of density in crystallography is current the main source and very useful, but its important to have cases where the nature of the disorder has been established by other means, such as NMR. 4. Some targets will also be used to test methods of structure refinement. In these cases, the best model received for a target will be released to the refinement community, who will subsequently submit new models. This too is an area where there have been some exciting developments in the last year, so we are hoping for significant progress. Refinement targets are selected based on the nature of the errors in the initial models. Because of the extended process, these targets need to be available for longer before release of the experimental structure. For those of you who have not provided targets to CASP before, the procedure is simple. There are three ways to submit targets: (1) Go the target submission web page and fill in the easy form; (2) When you submit your co-ordinates to the PDB, tick the 'CASP HOLD' box, automatically setting up a target entry; (3) Send an email the prediction center with details. If you have queries, there is a very experienced prediction center staff to deal with them. The key thing is timing: We need a window of at least four weeks between receiving information about a target and the release of your experimental structure. A longer window -- up to eight weeks - is often useful, for example so that a target can be used to test refinement methods, but is not essential (note that using the PDB target submission route automatically selects eight weeks). We don't need your experimental structure in advance of its release by the PDB, provided that will happen by the end of August. Please consult the target submission page for more details: http://www.predictioncenter.org/casp10/targets_submission.cgi There are already over 200 prediction teams signed for CASP 10, and so any targets provided will receive plenty of attention. If you have a suitable target now, we are ready to receive it. If new targets come up before July 17, we would also love to have them. (After July 17, we will continue with CASP ROLL for novel folds and membrane proteins). So please get in touch whenever a suitable opportunity arises, and help improve modeling methods. Thanks, CASP organizing committee John Moult, IBBR, University of Maryland, USA Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis, USA Torsten Schwede, SIB & Biozentrum University of Basel, Switzerland Anna Tramontano, University of Rome, Italy Get in touch: casp(a)predictioncenter.org More information: http://www.predictioncenter.org/casp10/index.cgi CASP Roll targets so far: http://www.predictioncenter.org/casprol/targetlist.cgi Submit a target: http://www.predictioncenter.org/casp10/targets_submission.cgi 1. Critical assessment of methods of protein structure prediction (CASP)--round IX. <http://www.ncbi.nlm.nih.gov/pubmed/21997831> Moult J, Fidelis K, Kryshtafovych A, Tramontano A. Proteins. 2011;79 Suppl 10:1-5. doi: 10.1002/prot.23200. Epub 2011 Oct 14. 2. CASP9 results compared to those of previous CASP experiments. <http://www.ncbi.nlm.nih.gov/pubmed/21997643> Kryshtafovych A, Fidelis K, Moult J. Proteins. 2011;79 Suppl 10:196-207. doi: 10.1002/prot.23182. Epub 2011 Oct 14 3.Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. <http://www.ncbi.nlm.nih.gov/pubmed/22020785> Kryshtafovych A et al. Proteins 2011;79 Suppl 10:6-20. doi: 10.1002/prot.23196. Epub 2011 Oct 21.

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