- phenixbb - phenix-online.org

Rwork Rfree gap by bust and phenix
by Zheng Zhou 02 Mar '16

02 Mar '16

Dear phenix experts, I have sent the question to the buster discussion board one week ago. I think I'd better consult this problem on the active phenix discussion board. I recently solved a P1 crystal structure, 6 fold NCS at 1.6 angstrom resolution. I used lattice symmetry to generate test set in phenix. The phenix.refine gave me Rwork/Rfree = 0.1828/0.2081. There are pieces of positive and negative density for the compounds. So I tried buster refinement with autoncs, TLS. The density for the compounds are much improved, no obvious positive density. However, It generated Rwork/Rfree = 0.1801/0.1912. I also find similar R factor examples at the similar resolution in the buster wiki: https://www.globalphasing.com/buster/wiki/index.cgi?AutoBusterExample4chawa… Would the small gap between Rwrok and Rfree be an issue? I have not deposited buster refined PDB yet, would this acceptable? Any reference to help if any reviewer questions about the small gap? Thanks for your advice in advance. Best, Zheng

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Re: [phenixbb] phenix.elbow with GAMESS
by Dyda 01 Mar '16

01 Mar '16

Dear Nigel, I agree, but pdb is what I have. I should think that the quality of the input should not impact whether .cif is output or not. The end of .gam: COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ CR 24.0 0.1912339815 -0.0759848760 -0.0714344444 O 8.0 2.3234578345 -0.2357845497 -0.1508067587 O 8.0 -0.7105232282 0.0098034893 1.8036685126 O 8.0 1.2076867850 -0.3346443692 -1.7335283981 O 8.0 -0.5260639033 1.7906968578 0.3539796904 O 8.0 0.9068338690 -1.9599479901 -0.6296444533 O 8.0 -1.9397708185 -0.1141525894 0.1891144601 C 6.0 2.8515146213 -0.0055174102 1.1989521238 C 6.0 1.9707450903 -0.6979131843 2.5449414024 C 6.0 0.4359449408 -0.0451724719 2.8465226464 C 6.0 3.0118766316 1.4363395032 1.6481146467 C 6.0 -0.0653144611 0.1564048347 4.4949200023 C 6.0 0.6249516515 0.4233319450 -2.8992641137 C 6.0 0.1643384668 2.4470081023 -2.2535061934 C 6.0 -0.9128640701 2.5088690737 -0.8469830060 C 6.0 1.5743374229 0.5462852223 -3.8500329514 C 6.0 -1.2118325877 3.9283584299 -0.4940679455 C 6.0 -0.1968029455 -3.0386081819 -0.8007813286 C 6.0 -1.6882650231 -2.4665688184 -1.2935287464 C 6.0 -2.6276161825 -1.2806785380 -0.2996777905 C 6.0 -0.3391479898 -3.6453123923 0.6022767778 C 6.0 -4.1453203443 -1.5862494692 0.1854244826 H 1.0 3.8553615186 -0.4420315035 1.2332199192 H 1.0 2.2818981212 -1.6647647766 3.1911897462 H 1.0 1.9667722755 1.9810594320 1.6970399031 H 1.0 3.6823942975 1.6618943249 2.5365171626 H 1.0 3.6238703905 1.9113333115 0.7438740891 H 1.0 0.8971167594 0.4695270592 5.1329947121 H 1.0 -0.6645891831 1.2206664940 4.5846682936 H 1.0 -0.6246971002 -0.6219821332 4.8583146656 H 1.0 -0.2487681929 -0.1134304045 -3.2439960069 H 1.0 1.1860397915 3.0186834522 -2.1641816248 H 1.0 -0.3750591440 2.8925729326 -3.2804399647 H 1.0 -1.9371292026 2.0739333624 -1.0806155814 H 1.0 1.9496290579 -0.6216286700 -4.2730835081 H 1.0 2.4497745286 1.0199721671 -3.6228827183 H 1.0 1.0277269687 0.9853088788 -4.8324755816 H 1.0 -1.6488875565 4.5338413808 -1.4704889855 H 1.0 -1.7951603842 3.9656768136 0.3514485986 H 1.0 -0.2983062508 4.5239905524 -0.4318350930 H 1.0 0.1219656972 -3.8775516930 -1.5693737575 H 1.0 -2.2141859609 -2.6816187114 -2.2405875656 H 1.0 0.7133579392 -3.9124935444 1.0380228614 H 1.0 -0.7783653014 -2.9666445248 1.3120392457 H 1.0 -0.9150821609 -4.6238970562 0.5814496583 H 1.0 -4.2320258907 -2.8021018481 0.2370382406 H 1.0 -4.7833967302 -1.1881592471 -0.7055025179 H 1.0 -4.4126745266 -1.1246420328 1.0220077683 ******************** 1 ELECTRON INTEGRALS ******************** ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 0.1 ( 0.0 MIN) TOTAL WALL CLOCK TIME= 0.1 SECONDS, CPU UTILIZATION IS 100.00% ------------- GUESS OPTIONS ------------- GUESS =HUCKEL NORB = 0 NORDER= 0 MIX = F PRTMO = F PUNMO = F TOLZ = 1.0E-08 TOLE = 1.0E-05 SYMDEN= F PURIFY= F INITIAL GUESS ORBITALS GENERATED BY HUCKEL ROUTINE. HUCKEL GUESS REQUIRES 649929 WORDS. SYMMETRIES FOR INITIAL GUESS ORBITALS FOLLOW. BOTH SET(S). 94 ORBITALS ARE OCCUPIED ( 30 CORE ORBITALS). 31=A 32=A 33=A 34=A 35=A 36=A 37=A 38=A 39=A 40=A 41=A 42=A 43=A 44=A 45=A 46=A 47=A 48=A 49=A 50=A 51=A 52=A 53=A 54=A 55=A 56=A 57=A 58=A 59=A 60=A 61=A 62=A 63=A 64=A 65=A 66=A 67=A 68=A 69=A 70=A 71=A 72=A 73=A 74=A 75=A 76=A 77=A 78=A 79=A 80=A 81=A 82=A 83=A 84=A 85=A 86=A 87=A 88=A 89=A 90=A 91=A 92=A 93=A 94=A 95=A 96=A 97=A 98=A 99=A 100=A 101=A 102=A 103=A 104=A ...... END OF INITIAL ORBITAL SELECTION ...... CPU 0: STEP CPU TIME= 0.24 TOTAL CPU TIME= 0.3 ( 0.0 MIN) TOTAL WALL CLOCK TIME= 0.4 SECONDS, CPU UTILIZATION IS 86.49% ---------------------- AO INTEGRAL TECHNOLOGY ---------------------- S,P,L SHELL ROTATED AXIS INTEGRALS, REPROGRAMMED BY KAZUYA ISHIMURA (IMS) AND JOSE SIERRA (SYNSTAR). S,P,D,L SHELL ROTATED AXIS INTEGRALS PROGRAMMED BY KAZUYA ISHIMURA (INSTITUTE FOR MOLECULAR SCIENCE). S,P,D,F,G SHELL TO TOTAL QUARTET ANGULAR MOMENTUM SUM 5, ERIC PROGRAM BY GRAHAM FLETCHER (ELORET AND NASA ADVANCED SUPERCOMPUTING DIVISION, AMES RESEARCH CENTER). S,P,D,F,G,L SHELL GENERAL RYS QUADRATURE PROGRAMMED BY MICHEL DUPUIS (PACIFIC NORTHWEST NATIONAL LABORATORY). -------------------- 2 ELECTRON INTEGRALS -------------------- DIRECT SCF METHOD SKIPS INTEGRAL STORAGE ON DISK. DIRECT TRANSFORMATION SKIPS AO INTEGRAL STORAGE ON DISK. ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 0.3 ( 0.0 MIN) TOTAL WALL CLOCK TIME= 0.4 SECONDS, CPU UTILIZATION IS 86.84% -------------------------- RHF SCF CALCULATION -------------------------- NUCLEAR ENERGY = 2520.5794603055 MAXIT = 199 NPUNCH= 2 EXTRAP=T DAMP=T SHIFT=F RSTRCT=F DIIS=F DEM=F SOSCF=T DENSITY MATRIX CONV= 2.00E-05 SOSCF WILL OPTIMIZE 16544 ORBITAL ROTATIONS, SOGTOL= 0.250 MEMORY REQUIRED FOR RHF ITERS= 640658 WORDS. DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 SCHWARZ INEQUALITY OVERHEAD: 30854 INTEGRALS, T= 0.00 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE ORB. GRAD VIR. SHIFT DAMPING INTEGRALS SKIPPED 1 0 0 -2059.2212832191 -2059.2212832191 0.988797951 0.000000000 0.000000000 1.000000000 191835514 22895770 2 1 0 -2042.8253644320 16.3959187871 1.142306775 0.674963723 0.000000000 1.000000000 192284889 22920383 3 2 0 -2053.1297307637 -10.3043663316 0.401569267 0.408533345 0.000000000 54.508125229 192386468 22914751 4 3 0 -2054.8896748699 -1.7599441062 0.681705613 0.974133914 0.000000000 3.406757827 185808214 23658736 ---------------START SECOND ORDER SCF--------------- 5 4 0 -2060.2884381280 -5.3987632581 1.089757171 0.228307597 0.000000000 0.000000000 191024572 23175415 6 5 0 -2062.5678087125 -2.2793705845 0.335341404 0.164617327 0.000000000 0.000000000 191517675 23118064 7 6 0 -2063.0509541215 -0.4831454090 0.503307418 0.129756838 0.000000000 0.000000000 189580417 23389152 I think the coords are the final config. Thanks for your help, Fred [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

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phenix.elbow with GAMESS
by Nigel Moriarty 01 Mar '16

01 Mar '16

Fred Does the .gam have a final geometry? You'll need to check because performing a QM geometry minimisation is not straight forward. BTW. A PDB file is the lowest quality input format. It's recommended that you try for a most information rich input such as SMILES or mol2. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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5th International Symposium on Diffraction Structural Biology (ISDSB2016)
by Leighton Coates 01 Mar '16

01 Mar '16

Hi All On behalf of the organizing committee, I am pleased to announce the “5th International Symposium on Diffraction Structural Biology” (ISDSB2016). The Symposium will take place on Sunday, August 7, 2016 through Wednesday, August 10, 2016 in Knoxville, Tennessee, USA. This symposium will report on the latest discoveries in structural biology using X-ray, neutron, and electron diffraction, and complementary techniques such as small-angle scattering, nuclear magnetic resonance spectroscopy, electron microscopy, and advanced computational approaches. Scientific insights at the molecular level allow structure guided drug discovery and protein engineering for improved biocatalysis. This basic research is important for supporting applications in the pharmaceutical industry and for new, sustainable, and environmentally friendly approaches to the production of chemical reagents and biofuels. Session topics include: Bioenergy Drug Design Enzyme Mechanism and Allostery Macromolecular Complexes Membranes and Membrane Proteins New Instruments and Methods Sources and Facilities A list of confirmed, invited speakers can be found on the conference web pages. The Symposium will be accompanied by two optional 1-day workshops on August 6, focused on Neutron Protein Crystallography and on Small-Angle Scattering, respectively. Please visit the conference website for further information: https://conference.sns.gov/event/2/ Thanks Leighton

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Command line version of Reflection_file _editor
by Rahel Woldeyes 29 Feb '16

29 Feb '16

Hi all, I was wondering if anyone has implemented command line compatible version of phenix.reflection_file_editor . Thanks! Rahel

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Command line version of Reflection_file _editor
by Rahel Woldeyes 29 Feb '16

29 Feb '16

Hi all, I was wondering if anyone has implemented command line compatible version of phenix.reflection_file_editor . Thanks!

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Simulated annealing composite omit map
by Appu kumar 29 Feb '16

29 Feb '16

Hello All, I am trying to make the simulated annealing composite omit map for a protein ligand complex at 4.37A resolution. I think, Simulated annealing is harsh and rendering the protein distorting a lot as is evident from the helix turning into the some random structure. In order to avoid this protein distortion in protein backbone, do I need to fix some weight or specific parameter or provide reference structure and put harsh weight ? Any advice or suggestions would be much appreciated. Appu

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Phaser-EP log file
by Nishant Pandey 28 Feb '16

28 Feb '16

Hi,I have a confusion regarding solving iodine SAD-data in Phaser-EP.1. GUI result shows Log-likelihood gain: 115037.70 and FOM: 0.527. But in log file SAD Refinement Table (Sorted) ----------------------------- SET SpaceGroup FOM Log-Likelihood Rfac Composition I # 1 P 21 21 2 0.53 -115038 69.4 23 Why there is negative value of Log-Likelihood in log file? Is Log-Likelihood and Log-likelihood gain is two different things?Has Phaser solved it? When I feed these results to Autobuild, the model was ~80 % complete with Rfree and Rwork of 0.3171 and 0.2754 and Model Map correlation 0.74. Model was further refined in phenix.refine upto Rfree = 0.27. 2. When I am solving same dataset with Autosol and Autobuild, the dimer orientation have changed? Is this 'normal' or one of the solution is wrong and if it then which one should choose to refine further? Thanks in advance.

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phenix.elbow with Gamess, no cif restraint file
by Dyda 26 Feb '16

26 Feb '16

Hi All, I'm clearly doing something wrong, but don't know what. Trying to run elbow with Gamess from the command line for "myligand" but no .cif file is produced. The input is a pdb file of the ligand, this the best I have. The command line: phenix.elbow --all-residues --do-all --gamess --basis=3D"3-21G" myligand.pdb > elbow.out & Everything seems to be OK, Gamess is found and run: > more elbow.out ------------------------------------------------------------------------------ electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.10.1-2155 None - Nigel W. Moriarty (NWMoriarty(a)LBL.Gov) ------------------------------------------------------------------------------ Random number seed: 3628800 Initial processing time : 0.01 seconds 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing P Input format is PDB MoleculeClass : C:15 O: 6 Cr: 1 (PDB format) 22 atoms 0 bonds 0 angles 0 dihedrals 0 rings 0 chirals Predicted memory usage by semi-empirical method : 41Mb Timing estimates Python portion / ATP : 62% c++ optimisation cycle / ATP : 47% Hydrogens may be required to determine the correct bonding Residue has metal at the centre of a coordination sphere. Using input geometry to generate restraints. Hydrogens may not be added. 0:10 Hydrogenise Hydrogenise Hydrogenise Hydrogenise Hydrogenise Hydrogenise H 1:49 ReCentre molecule for optimisation ReCentre molecule for optimisation ReC Optimisation software : GAMESS Quantum method : UHF Quantum basis set : 3-21G Opt steps : 60 Opt macro steps : 3 Searching for flowchart file: flowchart.py searching: /usr/local/apps/Phenix/1.10.1-2155/phenix-1.10.1-2155/modules/elbow ****************************************************************************** filename : /usr/local/apps/Phenix/1.10.1-2155/phenix-1.10.1-2155/modules/elbow/flowchart.py FOUND ****************************************************************************** searching: /usr/local/apps/Phenix/1.10.1-2155/phenix-1.10.1-2155 searching: /home/dyda/.elbow searching: /home/dyda searching: /spin1/users/dyda/myligand Machine has 24018 Mb total memory 14687 Mb free memory Setting 1000 Mb max memory usage Searching for template run file: GAMESS.csh searching: /spin1/users/dyda/myligand ****************************************************************************** filename : /spin1/users/dyda/myligand/GAMESS.csh FOUND ****************************************************************************** Using /spin1/users/dyda/myligand/GAMESS.csh as input run file template all .inp, .dat, .gam files are produced, no errors, but no cif file. Thanks. Fred [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

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script to calculate phase error
by Kaushik Hatti 25 Feb '16

25 Feb '16

Hello, I understand Phase error is written out after phenix.refine. For a particular case, I need to calculate phase error during different stages of model building (before refinement). Is there a script available which could calculate phase error given a model(PDB) and structure factors (MTZ) files? Thanks, Kaushik -- Stupidity is everyone’s birthright. However, only the learned exercise it! --Kaushik (28Oct2014)

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