- phenixbb - phenix-online.org

Feature request: multi-stage refinement protocols from the GUI?
by Tristan Croll 12 Mar '16

12 Mar '16

Hi all, I'm personally a big fan of the Phenix GUI, in particular for its automated record keeping for different runs. One thing I really wish it had, though, is the option to define more complex refinement scenarios as a single run. An example of what I'm talking about is the following protocol that has been working very well for me on a 3.6 Å strucutre: - ~6 rounds of refinement of TLS, a single group B-factor and occupancies (the latter for a very small set of residues, mostly low-occupancy lead ions) with positions fixed - ~8 rounds of TLS and individual B-factor refinement, still with positions fixed and with no further occupancy refinement - ~8 rounds of TLS, B-factor and position refinement with torsion-angle restraints to the starting model - ~8 rounds of position refinement with no restraints other than standard stereochemistry and metal bonds. I know that all of this could be scripted quite easily from the command line, but it would be fantastic to be able to queue up such a protocol as a single continuous job in the GUI. Best regards, Tristan

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Re: [phenixbb] Fluorescence group of eYFP
by miyatake 09 Mar '16

09 Mar '16

Hello, now I found a solution like below; 1) make links using " Extensions > Modeling > Make Link " in Coot 2) Do Ready_Set using the PDB file, and you'll get cif and link.edits files 3) Delete all the lines which contain OXT in the cif file. 4) Involve the cif and link.edits files to the Phenix.refine job It will work well for the CR2 containing GFP proteins. Best, Miyatake On Tue, 08 Mar 2016 15:00:29 -0800 André Hoelz <hoelz(a)caltech.edu> wrote: > Have you found a solution that works now? I have noticed the same problem that the OXT atom is incorporated and no bond is formed. I would be grateful if you share your a solution. > > Sent from my BlackBerry 10 smartphone. > Original Message > From: miyatake > Sent: Monday, March 7, 2016 11:07 PM > To: Pavel Afonine > Cc: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Fluorescence group of eYFP > > Dear Pavel, > > Thank you for your e-mail. > > The bonds I want to connect are between CR2 and amino acids like below; > > C PHE A 64 N1 CR2 A 66 > C3 CR2 A 66 N LEU A 68 > > so I made links by the "make link" of Coot. > > Then I made .cif file by the Ready_Set, but I noticed > it always contained OTX terminator atom of CR2, so the CR2 connections > to the next amino acids were something wrong after refinement if I used the cif > as it was. > > Thus I deleted OTX in the cif file, and then in turn it went well. > > I wonder why the cif file contained OTX, is it something a bug? > > Thank you for your attention. > > Miyatake > > > > On Mon, 7 Mar 2016 08:40:21 -0800 > Pavel Afonine <pafonine(a)lbl.gov> wrote: > > > Hi Miyatake, > > > > could you please send me (and copy to Nigel) the PDB file (and any > > ligand CIF files you use) and tell what bonds you are expecting to have > > and that brake as result of refinement. > > > > Thanks, > > Pavel > > > > On 3/7/16 03:40, miyatake wrote: > > > Dear all, > > > > > > I'm trying to a mutant of eYFP, which has fluorescence group, > > > CR2. > > > > > > During the refinement, however, the bonds between the CR2 and other amino acids > > > were cleaved even I added the cif file created by the ReadySet. > > > > > > > > > Would some one give me suggestions to solve the problem? > > > > > > Miyatake > > > > > > _______________________________________________ > > > phenixbb mailing list > > > phenixbb(a)phenix-online.org > > > http://phenix-online.org/mailman/listinfo/phenixbb > > > Unsubscribe: phenixbb-leave(a)phenix-online.org > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

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Re: [phenixbb] 7th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 08 Mar '16

08 Mar '16

Second announcement 7th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. May 16 - May 20, 2016 Detailed information can be found on the workshop web page: https://conference.sns.gov/event/15 Application deadline: April 1, 2016 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome. However the course organization is not able to support travel or accommodation. The number of participants will be limited to 15. There is no registration fee for all selected participants. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (for graduate students only; 1/2 to 1 page), should be sent electronically to meilleurf(a)ornl.gov<mailto:[email protected]> before April 1, 2016. Flora Meilleur, Ph. D Associate Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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Wrong stereochemical restraint of Hyp
by YANG HAI 07 Mar '16

07 Mar '16

Dear Phenix Developers, I was refining a structure containing L-hydroproline (HYP) and it looks like that the dictionary for HYP in Phenix has the wrong stereochemical restraint. I modeled as L-hydroxylproline (trans) but the phenix.refine always flipped the hydroxyl group and ended up as L-allo-hydroxylproline (cis). I created a .cif file and the issue is resolved, but it would be nice if the restraint can be fixed in the next version of Phenix. Thanks a lot Yang Hai Department of Chemistry, University of Pennsylvnia

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Constrained groups for occupancy refinment
by Jan Abendroth 07 Mar '16

07 Mar '16

Hi all, I have a case where a residue is in two alternative conformations for chain A and chain B. This residue (Arg 62) happens to be close to its NCS mate, such that only conformations A for both chains or only conformations B can take place at the same time. I tried to follow guidance from the CNG newsletter 2015/07 and set up the constrained groups as shown below. However, the refinement crashes with an AtomSelectionError. Any ideas what I could have done differently? Cheers, Jan refinement { refine { occupancies { constrained_group { selection = chain A and resseq 62 and altloc A or \ chain B and resseq 62 and altloc A or selection = chain A and resseq 62 and altloc B or \ chain B and resseq 62 and altloc B or } } } } -- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com

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Phenix omit maps
by wtempel 05 Mar '16

05 Mar '16

Hello all, is the output of phenix.maps with maps.omit.selection=(resname LIG) equivalent to removal of LIG atoms from coordinates and subsequent map calculation with an empty maps.omit.selection? What, if any, measures of bias removal are applied in the process of map calculation, absent any explicit efforts by the user to modify coordinates? Thank you, Wolfram Tempel

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iNEXT
by Anastassis Perrakis 03 Mar '16

03 Mar '16

Dear all, iNEXT is a Horizon2020 project aiming to allow international users transnational access to infrastructures for Structural Biology, with an emphasis on new users, and a focus on translational research projects in biomedicine, biotechnology and biomaterials. http://www.inext-eu.org For the first time, iNEXT offers coordinated access to NMR, EM, X-ray crystallography and biophysical methods. There are specific access routes for expert users and new users, and for the different techniques. These are becoming gradually available as the project proceeds, and you should expect regular updates. For now you can apply for access to some of the planned modalities, namely: Structural Audit: mail-in your protein sample for quality analysis including stability, dispersity, crystallisation and SAXS Cryo-EM sample optimisation: to move from negative stain to cryo-EM Macromolecular interactions: for accessing biophysical equipment and expertise to quantify macromolecular interactions Synchrotron data: for access to some of the best beamlines in Europe High-field NMR: or access to some of the most powerful NMR machines in Europe High-resolution EM: : for access to some of the best microscopes in Europe For more details please see: http://www.inext-eu.org/access/ with best regards from the iNEXT team, Tassos Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

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Remove distant restraint between two atoms
by Blankenfeldt, Wulf 03 Mar '16

03 Mar '16

Dear all, I would like to unrestrain the distance between two atoms in a ligand – how can I do this? I found instructions for writing a remove_restraints_selections.params file in the phenix.refine manual, but it does not seem to address bond distances. Thank you in advance, Wulf ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie" 50 Jahre Spitzenforschung - 50 Jahre HZI: www.helmholtz-hzi.de/50 Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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Rwork Rfree gap by bust and phenix
by Zheng Zhou 03 Mar '16

03 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 02 Mar '16

02 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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