- phenixbb - phenix-online.org

Set up phenix and rosetta for phenix.rosetta_refine
by Yonglin Hu 17 Mar '16

17 Mar '16

Hello List, I would like to perform phenix.rosetta_refine on a structure. I understand that to use this program, I need to set up phenix and rosetta installations separated from those used in MR_Rosetta. I installed the most recent phenix and rosetta and followed the online documents, but when I tried to run "rosetta.build_phenix_interface", the program failed immediately with the following error messages: False scons: Reading SConscript files ... Running versioning script ... fatal: Not a git repository (or any of the parent directories): .git Done. (0.0 seconds) Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site CalledProcessError: Command '['./update_options.sh']' returned non-zero exit status 1: File "/usr/local/rosetta-refine/rosetta/main/source/SConstruct", line 172: main() File "/usr/local/rosetta-refine/rosetta/main/source/SConstruct", line 163: SConscript("SConscript", "build") File "/usr/local/rosetta-refine/rosetta/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614: return method(*args, **kw) File "/usr/local/rosetta-refine/rosetta/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551: return _SConscript(self.fs, *files, **subst_kw) File "/usr/local/rosetta-refine/rosetta/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260: exec _file_ in call_stack[-1].globals File "/usr/local/rosetta-refine/rosetta/main/source/SConscript", line 28: subprocess.check_call(["./update_options.sh"]) File "/usr/local/rosetta-refine/phenix-dev-2328/base/lib/python2.7/subprocess.py", line 540: raise CalledProcessError(retcode, cmd) These messages are not very informative and I don't know what to do next. Any help will be greatly appreciated. Yonglin Hu

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on b-factor refine
by Smith Liu 15 Mar '16

15 Mar '16

Dear All, I just read a paper on phenix refine, which contains content "B-factor refinement (two groups per residue) ". Here the "two groups per residue" should be accomplished by the phenix command line rather than the GUI, right? And if right, will you please let me know the command for "two groups per residue" for B-factor refine? Smith

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Real space difference maps?
by Oliver Clarke 15 Mar '16

15 Mar '16

Hello, is there any possibility of (or current plan for) including the capacity in a future PHENIX release to calculate a residual map automatically after phenix.real_space refine, (i.e. simulating a map from the model incorporating corrections for B-factor variation and calculating a difference map with the experimental map)? This would be very convenient when building into EM maps. Cheers, Oli

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Postdoc position available at LBNL
by Peter Zwart 14 Mar '16

14 Mar '16

Berkeley Lab's Molecular Biophysics and Integrated Bioimaging Division is looking for a Computational Biologist to work on the development of computational and experimental methodologies for Fluctuation X-ray Scattering (FXS; *http://bit.ly/1W6SONZ* <http://bit.ly/1W6SONZ>) and associated biophysical techniques, such as SAXS/WAXS and Single Particle diffraction. The candidate will be involved in the development and expansion of the underlying theory of FXS, either as a standalone technique or in a hybrid capacity, and will aid in its practical deployment. For details, have a look here: https://lbl.taleo.net/careersection/jobdetail.ftl?job=82189&lang=en#.Vubva0… Regards Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Staff Scientist Berkeley Center for Structural Biology, Science lead Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CAMERA: http://camera.lbl.gov/ -----------------------------------------------------------------

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phenix autosol
by Vandna Kukshal 13 Mar '16

13 Mar '16

Hi , I am solving a structure using selenium SAD using autosol. Autosol gave me nice solution but many loop and side chain density is missing. autosol gave me many different output MTZ files . for building further in coot which MTZ file i should use and for refinement in phenix refinement which MTZ file i should use . I tried doing refinement with .sca file it gave me increase Rfree afte single cycle of refinement . thanks for your suggestions. -- Vandna Kukshal Postdoctral Research Associate Dept. Biochemistry and Molecular Biophysics Washington University School of Medicine 660 S. Euclid, Campus Box 8231 St. Louis, MO 63110

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Feature request: multi-stage refinement protocols from the GUI?
by Tristan Croll 11 Mar '16

11 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 04 Mar '16

04 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 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

1 0

script to calculate phase error
by Kaushik Hatti 26 Feb '16

26 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)

2 2

Separate cif files for the same nucleoside analog in it's monophosphate or triphosphate form?
by Zhe Li 26 Feb '16

26 Feb '16

Hi, I’m working on several protein/ligand structures, where the ligand is a novel nucleoside analog inhibitor. In each structure the ligand is either non-covalently bound as a ligand-5’-triphosphate (TP), or covalently bound to the protein as ligand-5’-monophosphate (MP). Do I need to create different cif file for ligand-MP and ligand-TP, or phenix can recognize the phosphates and there is no need for that? Thank you.

3 2

Multiple conformations
by Alejandro Virrueta 25 Feb '16

25 Feb '16

This is not exactly phenix specific, but I was wondering what are some commonly used methods to determine and validate the presence/occurrence of multiple conformations for a given amino acid? I am currently refining (for 5 cycles) a pdb with the occupancy of atoms of a specific residue set to 0, and then looking at the difference density map contoured to 3 sigma for extra density. Is this somewhat correct? What else could/should I do? Would using OMIT maps help? (What are OMIT maps, and how do I generate them?) Thanks, Alex (not a crystallographer)

4 4

How to include restrains to DNA as A-DNA or B-DNA
by Zhe Li 23 Feb '16

23 Feb '16

I am refining a protein-dsDNA complex structures at 2.4-3 A. Based on the phosphate distance, I can predict if particular nucleotide is A DNA (C3’-endo) or B DNA (C2’-endo). I want to add restrain to to the specific nucleotides as A or B DNA. But secondary_structure_restraints for nucleic acid does not seem to have options for this. Any suggestions? Thanks

3 2

Course on “Integrating X-ray crystallography and scattering with electron microscopy” - Oeiras (Portugal)
by Jose Artur Brito 23 Feb '16

23 Feb '16

Dear Colleagues, we hereby announce a 4-day course on “Integrating X-ray crystallography and scattering with electron microscopy”. The course is funded by i-NEXT and will be held at NOVA ITQB, Oeiras (nearby Lisbon), Portugal, May 2 to 5, 2016. The course covers a multidisciplinary approach to study the structure of challenging proteins, focusing on membrane proteins and large complexes. The basic principles will be provided for each addressed technique (Macromolecular Crystallography, Mass Spectrometry and Electron Microscopy); their applications in biological systems, major benefits and limitations will also be discussed. The Workshop is organized with lectures in the mornings followed by hands-on training. The course is aimed primarily at PhD students and young Post-Doctoral researchers interested in Structural Biology. Confirmed speakers are Jose Maria Carazo, Dmitri Svergun and Isabel de Moraes. Participants will be limited to 20. Candidate selection will be based on a short CV, a motivation letter from the applicant, and a recommendation letter from the supervisor. Registration deadline is February 23. Please send your application to combstruct2016(a)itqb.unl.pt. Registration fee is 180Eur including accommodation. More information can be found at http://www.itqb.unl.pt/combstruct2016 The Organizers, Margarida Archer, José A. Brito (ITQB-UNL) and Jose Maria Carazo (CNB-CSIC) -- ************************************************** * Jose Artur Brito, PhD * * Post-Doctoral Fellow * * Membrane Protein Crystallography Laboratory * * Instituto de Tecnologia Quimica Biologica * * Avenida da Republica, EAN * * 2780-157 Oeiras * * PORTUGAL * * * * Telephone - +351 214 469 761 * * Mobile - +351 962 452 179 * * Fax - +351 214 433 644 * * * * E-mail - jbrito(a)itqb.unl.pt * * Website - http://mx.itqb.unl.pt/ * **************************************************

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CCP4 crystallographic summer school at the APS, June 21 - 29, 2016
by Sanishvili, Ruslan 23 Feb '16

23 Feb '16

Dear Colleagues, We are pleased to announce the 9th annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Title: CCP4 crystallographic school: From data collection to structure refinement and beyond Dates: June 21 through 29, 2016 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop the first three days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Crystallographic computation workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on, interactive trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 21. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Registration fees: The registration fee for the selected participants is $400 for the academic and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

1 0

Rebuild fails in Rosetta-MR
by Rhys Grinter 23 Feb '16

23 Feb '16

Dear all, I'm currently trying to improve an model for a difficult MR problem using Rosetta-MR, When the program gets to the Rebuild stage it fails with the following message: *Error message:* child process stderr output: command: 'sh .../MR_ROSETTA_17/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/run_rebuild.sh"' .../MR_ROSETTA_17/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/run_rebuild.sh: line 5: 8996 Trace/BPT trap: 5 "/Applications/Rosetta/main/source/bin/mr_protocols.macosclangrelease" @"rebuild.flags" > "rebuild.log" 2>&1 Failed to run REBUILD Sorry: Failed to run REBUILD...see log file in .../MR_ROSETTA_17/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/rebuild.log Sorry: mr_rosetta failed... Sorry routine failed Please see log file for full error message *In the rebuild logfile:* dyld: lazy symbol binding failed: Symbol not found: ___sincos_stret Referenced from: /Applications/Rosetta/main/source/bin/mr_protocols.macosclangrelease Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___sincos_stret Referenced from: /Applications/Rosetta/main/source/bin/mr_protocols.macosclangrelease Expected in: /usr/lib/libSystem.B.dylib Has anyones experienced this error? Cheers, Rhys -- Dr Rhys Grinter Sir Henry Wellcome Fellow Monash University +61 (0)3 9902 9213 +61 (0)403 896 767

4 4

Problem refining structure, error message
by Natalia Ketaren 22 Feb '16

22 Feb '16

Hello, I’m building a structure at the moment, and I have since removed lithium ions from structure. However, when I go to refine using phenix, I get the error message: “No atom selected: name LI and Chain F and rename LI resseq 8” I’ve tried using earlier files, prior to my addition of lithium ions and I still get the same error message. I’m using Phenix version 1.10.1-2155-000 Could anyone help me overcome this error message? Cheers, Nat _____________________________ Natalia E. Ketaren, PhD Research Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: (212) 327-8136 Fax: (212) 327-7193 Natalia.Ketaren(a)rockefeller.edu<mailto:[email protected]> website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/

6 7

different occupancies for same molecule; optimize final model question
by Georg Mlynek 22 Feb '16

22 Feb '16

On 02/21/2016 11:33 PM, Georg Mlynek wrote: > Dear scientific community, > > 1. > > if I put in the gui under Modify selections for: Occupancies / simple > occupancy refinement > > resname SO4 > resname GOL > > > > phenix outputs different occupancies for each of the elements in the > molecule. > > > > Is the atom selection syntax wrong or is it a bug? (Ready set is also > not flagging or correcting this, would be nice is this can be implemented) > > 2. I used phenix optimize final model and I wonder why it refines K > anisotropic but not NA and CL. > (I would be very nice, if the program could summarize at the end which > settings and strategies were finally used, so this can be added to the > publication: I know it is under development) > > > adp { > individual { > isotropic = not (element K) > anisotropic = (element K) > } > > } > occupancies { > individual = resname NA or resname K or resname CL > remove_selection = None > constrained_group { > selection = None > } > > > I am using ubuntu 15.10 > > phenix version dev-2313-000 > > Many thanks in advance, best regards Georg.

2 1

Fwd: Alternative method to Phenix_mr_rosetta
by Henry Fang 19 Feb '16

19 Feb '16

Hi All, Our group is working on an ab initial density modification method to solve the phase problem. Last year, I applied the methods to the cases with a initial template which has already been correctly placed in the unit cell. I tried several cases in the Terwilliger, T. C., et al. (2012). "phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta". Starting from the templates provided in the http://www.phenix-online.org/phenix_data/terwilliger/rosetta_2011/ I can get a initial density map, then apply our method to reduce the phase difference to around 50° in the highest experiment data resolution. Now, I might want to try more blind cases with our methods. If we can solve more structures, that would be more convincing. Do you have some suggestions? Where could I find some more unsolved structures? I might need structures with placed template and high solvent content (at least above 50%). Thanks, Henry

2 1

Fwd: Generate difference electron density maps for residues with multiple conformations
by Alejandro Virrueta 18 Feb '16

18 Feb '16

Hello all, I am trying to get the difference electron density maps for residues with multiple conformations after I set the occupancy of their atoms to 0. My main goal is to visualize the green positive density peaks that should appear for the atoms whose occupancy I set to 0. However, when I run the phenix.refine command (doing all of this via cli, not gui), the output pdb file I will try to illustrate my process and problem with an example that works fine and one that doesn't, side by side, step by step. 1. I generate a pdb file that has a chosen residue set to occupancy 0. See 'pdb_1agy_res_SER_resID_120_del.pdb' and 'pdb_1agy_res_SER_resID_129_del.pdb'. As you can see, the former has SER 120 set to 0 occupancy and has one conformation, and the latter has SER 129 set to 0 occupancy for BOTH of its conformations. Both files are correct up to this point. 2. I then execute the following command: phenix.refine *pdb_del_file* *mtz_file* main.number_of_macro_cycles=5 output.write_eff_file=False output.write_geo_file=False output.write_def_file=False refinement.input.xray_data.r_free_flags.generate=True --overwrite - with *mtz_file *set to '1agy.mtz' (from the PDB) and *pdb_del_file* set to either 'pdb_1agy_res_SER_resID_120_del.pdb' and 'pdb_1agy_res_SER_resID_129_del.pdb'. - This results in 2 files pdb_1agy_res_SER_resID_XXX_del_refine_001.mtz and pdb_1agy_res_SER_resID_XXX_del_refine_001.pdb. Comparing these pdb files, you can see that the occupancy for SER 120 remains set to 0 (which is what I want), but the occupancies for the 2 conformers for SER 129 have been filled in by phenix (not what I want) somewhere during the refinement process. As a result, I get the desired difference peaks for SER 120, but not for SER 129 (which seems to be averaged out). Other than deleting the 2nd conformation for SER 129, is there a way to solve this problem, preferably via command line arguments/flags? Thanks, Alex

2 5

correct space group for phenix.merging_statistics?
by Murpholino Peligro 18 Feb '16

18 Feb '16

Hi. Is it really important to have the correct space group in the mtz (or XDS_ASCII.HKL) file which will be the input for phenix.merging_statistics? I have space group= 89 And I know it is space group=96 Thanks

3 5

Fwd: Sorry: Fatal problems interpreting model file
by Alejandro Virrueta 17 Feb '16

17 Feb '16

Hello, How can I successfully execute the following command: phenix.refine pdb_1jbe_res_ALA_resID_101_del.pdb 1jbe.mtz main.number_of_macro_cycles=5 output.write_eff_file=False output.write_geo_file=False output.write_def_file=False refinement.input.xray_data.r_free_flags.generate=True --overwrite Currently, I am getting the following error: Sorry: Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols: 8 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. I'm not a crystallographer, so I don't fully understand the error. I'm simply trying to automate this procedure for many PDBs, and this particular error has come up quite a few times. Can I resolve this issue by providing additional files or command line flags? Other files I have available are 1jbe.cif and 1jbe-sf.cif. File 'pdb_1jbe_res_ALA_resID_101_del.pdb' is similar to 1jbe.pdb, except that the occupancies for ALA 101 are set to 0. Thanks, Alex

2 1

Using phenix.real_space_refine with mmcif model?
by Oliver Clarke 16 Feb '16

16 Feb '16

Hello, Is it possible to use phenix.real_space_refine with mmcif input? When I attempt to run as "phenix.real_space_refine model.mmcif map.mrc" or "phenix.real_space_refine model.cif map.mrc" I get the error "Sorry: PDB file is needed", and looking at the documentation I cannot see how to explicitly specify the model (there is not "model" keyword or similar). Anybody have a way around this? Or is there a keyword I am missing? phenix.refine generally works fine with mmcif, but maybe real_space_refine has not been configured to do so yet? Would be helpful for large structures which break the regular pdb format if so. Cheers, Oli

2 1

Re: [phenixbb] Using PyMOL-1.8 with PHENIX-dev-2306
by acyang 16 Feb '16

16 Feb '16

Hi Billy Thanks for your reply. I installed phenix from source (phenix-installer-dev-2306-source.tar.gz). And I used scientific linux 7.1 for my workstation. I noticed that SCONS is adopted in the installation of phenix, and phenix will download a modified version of python (python_2.7.8_cci). I think the problem can be solved by adding a flag "--enable-unicode=ucs4" in configuring Python-2.7.8_cci. I'd appreciate if you can tell me how to modify the SCONS script file. by A.C. 2016-02-12 16:52 GMT+08:00 Billy Poon <bkpoon(a)lbl.gov>: > Hi, > > Are you installing phenix from source or from a binary distribution? And > which operating system are you using? I can give you the flags (in addition > to the --prefix flag for installing into the base directory) for the > configure step for either OS X or Linux. > > You can basically install Phenix normally, and then recompile our Python > from scratch with our regular flags and your extra flag. > > -- > Billy K. Poon > Research Scientist, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > 1 Cyclotron Road, M/S 33R0345 > Berkeley, CA 94720 > Tel: (510) 486-5709 > Fax: (510) 486-5909 > Web: https://phenix-online.org > > On Wed, Feb 3, 2016 at 3:05 AM, acyang <acyang0903(a)gmail.com> wrote: > >> Hi everyone >> >> I've installed pymol and phenix on my scientific linux7.1 workstation. >> I can launch pymol via the launching script($PYMOL_HOME/pymol) normally. >> But when I launched pymol in phenix GUI, I got some error as followed: >> >> ********************************************************************************************************************************* >> Traceback (most recent call last): >> File "/opt/PyMOL/modules/pymol/__init__.py", line 71, in <module> >> import pymol >> File "/opt/PyMOL/modules/pymol/__init__.py", line 521, in <module> >> import pymol._cmd >> ImportError: /opt/PyMOL/modules/pymol/_cmd.so: undefined symbol: >> PyUnicodeUCS4_SetDefaultEncoding >> >> ********************************************************************************************************************************* >> After STFW*, *I knew the problem is about unicode variant (UCS2, UCS4). >> I also checked the configuration of two python. >> For /bin/python (adopted by pymol) >> >> >>> import sys>>> print sys.maxunicode1114111 >> >> And for $PHENIX_HOME/base/bin/python (adopted by phenix) >> >>> import sys >> >>> print sys.maxunicode >> 65535 >> >> My question is : How do I add the flag --enable-unicode=ucs4 in configuring Python-2.7.8_cci. >> >> >> I'd appreciate if any reply on this. >> >> acyang >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > >

2 2

Specify space group with phenix.map_to_structure_factors?
by Oliver Clarke 16 Feb '16

16 Feb '16

Hi, I frequently use phenix.map_to_structure_factors to generate mtz files from EM maps for use in Coot - it is by far the best tool I have found for this purpose. For convenience (so I can easily build and refine one protomer of a four-fold symmetric entity), I often convert these mtz files from the default P1 to P4 spacegroup using CCP4, and I wonder if it would be possible to include an option to specify the output spacegroup directly in map_to_structure_factors (or perhaps it is there and I have missed it?)? Even better would be if there were a way to check the symmetry and refine the orientation of the input volume such that the map is centered in the unit cell and the symmetry axis of the volume is appropriately aligned - often I have aligned the input volume to another reference volume in Chimera, and if the alignment is not perfect the symmetry axis of the volume might be slightly misaligned from what would become the fourfold axis of the output. Cheers, Oli.

2 1

Update: Check for radiation-induced reduction of a disulfide bond
by Ezequiel Noguera 15 Feb '16

15 Feb '16

Sorry, my previous email was incomplete. My structure has negative density in the center of some disulfides (the magnitude of this effect vary between different monomers in the ASU). I'd like to refine the structure in an "artificial reduced form", where cysteines involved in disulfides are treated in reduced form, but repulsions originating from neighboring sulfur atoms are turned-off, to monitor distances (I expect that SG atoms remain close to 2 A), guided only by data. Thank you, Ezequiel

4 5

ensemble refinement
by George Kontopidis 15 Feb '16

15 Feb '16

Does ensemble refinement run on Phenix version 1.10.1-2155 (for windows) If yes can it run from GUI or only using command line? George

4 7

REASONS UNKNOWN
by Almudena Ponce Salvatierra 15 Feb '16

15 Feb '16

-- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

1 1

Re: [phenixbb] Arg, Glu, etc. naming conventions
by Mark A Saper 15 Feb '16

15 Feb '16

Apparently a torsion angle of –180° is considered very different from 0° because of the NH1.NH2 names. And the phenix convention is now different from coot. Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School New location: Room 3220B, MSRB III | saper(a)umich.edu | +1 (734) 764-3353 On Feb 14, 2016, at 4:07 PM, Eckhard Hofmann <eckhard.hofmann(a)bph.ruhr-uni-bochum.de> wrote: > Dear Mark, > I think Oleg is in the process of writing a little routine to fix problems in pdbs with regard to order of atoms in residues and such. Maybe fixing naming conventions could/will be included. > Cheers, > Eckhard > > > Am 14.02.2016 um 19:37 schrieb Mark A Saper: >> Phenix 1.10.1 is flagging several of my Arg residues with bad dihedral angles. Phenix is much more strict about NH1, NH2 naming conventions then 6 months ago. Can these be fixed with PDB Tools? How? Many thanks in advance. >> -Mark >> _________________________________ >> Mark A. Saper, Ph.D. >> Associate Professor of Biological Chemistry, University of Michigan >> Ann Arbor MI 48109-1055 U.S.A. >> saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > > -- > Prof. Dr. Eckhard Hofmann <eckhard.hofmann(a)bph.ruhr-uni-bochum.de> > Ruhr-Uni Bochum > AG Proteinkristallographie, LS Biophysik, ND04/318 > 44780 Bochum > Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762 > ORCID: 0000-0003-4874-372X

2 1

Arg, Glu, etc. naming conventions
by Mark A Saper 14 Feb '16

14 Feb '16

Phenix 1.10.1 is flagging several of my Arg residues with bad dihedral angles. Phenix is much more strict about NH1, NH2 naming conventions then 6 months ago. Can these be fixed with PDB Tools? How? Many thanks in advance. -Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

2 1

Check for radiation-induced reduction of a disulfide bond
by Ezequiel Noguera 13 Feb '16

13 Feb '16

I'm working with one protein, crystallized in oxidized form, which exhibits negative density in the Fo-Fc map at the center of the disulfide bond. As a test of radiation-induced reduction during data collection, I'd like to do a trial refinement described in a previous work from literature, where SG sulfurs of involved cysteines were refined without van der Waals interactions to monitor distances of these atoms. How can I do this calculation in Phenix? Thanks in advance

2 1

Using PyMOL-1.8 with PHENIX-dev-2306
by acyang 12 Feb '16

12 Feb '16

Hi everyone I've installed pymol and phenix on my scientific linux7.1 workstation. I can launch pymol via the launching script($PYMOL_HOME/pymol) normally. But when I launched pymol in phenix GUI, I got some error as followed: ********************************************************************************************************************************* Traceback (most recent call last): File "/opt/PyMOL/modules/pymol/__init__.py", line 71, in <module> import pymol File "/opt/PyMOL/modules/pymol/__init__.py", line 521, in <module> import pymol._cmd ImportError: /opt/PyMOL/modules/pymol/_cmd.so: undefined symbol: PyUnicodeUCS4_SetDefaultEncoding ********************************************************************************************************************************* After STFW*, *I knew the problem is about unicode variant (UCS2, UCS4). I also checked the configuration of two python. For /bin/python (adopted by pymol) >>> import sys>>> print sys.maxunicode1114111 And for $PHENIX_HOME/base/bin/python (adopted by phenix) >>> import sys >>> print sys.maxunicode 65535 My question is : How do I add the flag --enable-unicode=ucs4 in configuring Python-2.7.8_cci. I'd appreciate if any reply on this. acyang

2 1

reattach jobs
by andre.stiel 12 Feb '16

12 Feb '16

Hi, how do I reattach a job to a project in the GUI. Say I took the GUI to prepare a commands file (.eff) and save it. Then I run the actual refine from the command line on another computer using the save commands file. After the job is done, how do I get the job back in the GUI. I do not find something to „load“ or „reattach“ a job. Thanks. André André C. Stiel, Ph.D. (PI) +49 (0) 89 3187 3972 Office: Building 57, Room 009 Cell Engineering Group Institute of Biological and Medical Imaging Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen (komm.) Registergericht: Amtsgericht Muenchen HRB 6466 USt-IdNr: DE 129521671

2 1

phenix install error on linux
by Min Zheng 11 Feb '16

11 Feb '16

Dear All, I am installing phenix, and get the following error: ========================================================================== Phenix Installation version: 1.10.1-2155 machine type: intel-linux-2.6-x86_64 OS version: 3.11.10-29-default destination: /home/m/m_zhen01/phenix-1.10.1-2155 # of processors: 20 ========================================================================= Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 262, in <module> installer(sys.argv[1:]).install() File "/nfsexp/homes/m_zhen01/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py", line 185, in install self.install_from_binary() File "/nfsexp/homes/m_zhen01/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py", line 295, in install_from_binary self.reconfigure(log=log) File "/nfsexp/homes/m_zhen01/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py", line 460, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/nfsexp/homes/m_zhen01/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/installer_utils.py", line 81, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/home/m/m_zhen01/phenix-1.10.1-2155/base/bin/python /home/m/m_zhen01/phenix-1.10.1-2155/modules/cctbx_project/libtbx/configure.py --current_working_directory /home/m/m_zhen01/phenix-1.10.1-2155/build --command_version_suffix 1.10.1-2155 phenix phaser solve_resolve labelit' failed with exit code 1 m_zhen01@LIBRA:~/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5> /home/m/m_zhen01/phenix-1.10.1-2155/base/bin/python Traceback (most recent call last): File "/usr/lib64/python2.7/site.py", line 564, in <module> main() File "/usr/lib64/python2.7/site.py", line 546, in main known_paths = addusersitepackages(known_paths) File "/usr/lib64/python2.7/site.py", line 276, in addusersitepackages user_site = getusersitepackages(kind) File "/usr/lib64/python2.7/site.py", line 244, in getusersitepackages user_base = getuserbase() # this will also set USER_BASE File "/usr/lib64/python2.7/site.py", line 230, in getuserbase from sysconfig import get_config_var File "/usr/lib64/python2.7/sysconfig.py", line 10, in <module> 'stdlib': '{base}/'+sys.lib+'/python{py_version_short}', AttributeError: 'module' object has no attribute 'lib' Thanks in advance, Min

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Refinement differences?
by Mark A Saper 11 Feb '16

11 Feb '16

Hi, I used Phenix, build 2037 to refine a a new structure. I reran the refinement (with the identical parameters) in build 2155 (v1.10.1) and obtained different statistics and slightly worse geometry. Any idea why? In 2037: start final --------------------------------------- R-work: 0.2488 0.2244 R-free: 0.3003 0.2851 RMS(angles): 1.67 0.80 RMS(bonds): 0.020 0.004 Ramachandran outliers: 1.2% (Goal: < 0.2%) Ramachandran favored: 94.5% (Goal: > 98%) Rotamer outliers: 8.7% (Goal: 1%) C-beta outliers: 0 (Goal: 0) Clashscore: 3.14 Overall score: 2.19 2155 start final --------------------------------------- R-work: 0.2488 0.2331 R-free: 0.3003 0.2856 RMS(angles): 1.77 0.72 RMS(bonds): 0.020 0.004 Ramachandran outliers: 1.4% (Goal: < 0.2%) Ramachandran favored: 93.4% (Goal: > 98%) Rotamer outliers: 9.4% (Goal: 1%) C-beta outliers: 0 (Goal: 0) Clashscore: 4.10 Overall score: 2.36 _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

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differentiate Glu/Gln and Asp/Asn from Electron Density?
by Kaushik Hatti 11 Feb '16

11 Feb '16

Hello, In continuation to my earlier thread (subject: sequence independent model building possible?), I have built model into density without knowledge of sequence for a data diffracted to 1.9A resolution. Current R/Rfree is 15/19, phaser error=16.88 degrees with no Ramachandran outliers. Is there a way we can differentiate between Glu/Gln, Asp/Asn and sometimes Thr/Val directly from density? I have considered the local environment (hydrophobic/hydrophilic/polarity pockets, possible hydrogen bonds/other interactions, buried/exposed, etc...) in choosing one over the other confusing pairs of amino acids. However, I am not absolutely certain in many places. A BLAST of this sequence against all non-redundant protein sequence database yield highest hit of 80% sequence identity. Hence, we are still not sure of sequence of the contaminant protein which got crystallised and want to decipher sequence directly from the structure. Thanks for any pointers/suggestions, Regards, Kaushik -- Stupidity is everyone’s birthright. However, only the learned exercise it! --Kaushik (28Oct2014)

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Creating cyclic peptide coordinates and restraints
by A User 10 Feb '16

10 Feb '16

Hi Everyone, I am working on a 1.9A enzyme inhibitor complex. The inhibitor is a macrocyclic peptide with a non-proteinogenic amino acid that is modified at the n-terminus with a chloroacetyl-group that cyclizes via the sulfhydryl group of the next cysteine. The total lenght of the peptide is 9 amino acids. What is the most straight forward way to generate the coordinates of such macrocyclic peptide and what are the best settings in eLBOW to generate the restraints for it? Thanks for your time guys! Ben

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