- phenixbb - phenix-online.org

Partially occupied side chains in special position
by Nicholas Keep 06 Sep '12

06 Sep '12

I have an ARG which has nice density for its guanadinium group on a 2 fold. This is the same conformer from the two copies. The occupancy of this chain is set to 0.5 and a second conformer that does not cross the two fold is provided. There is clearly a repulsion term in phenix refines that moves the quanadinium away from the two fold. Do the atoms of the guanadinum group need to have an occupancy of 0.25? Can I specify no repulsion between these symmetry elements? Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.keep(a)mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door

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Adding H atoms - AssertionError
by Kristof Van Hecke 06 Sep '12

06 Sep '12

Dear, When I try to add H-atoms to a metal-coordination complex (not a protein, nor DNA) during refinement or via the ReadySet module, I get the following error: (I have a proper restraints .cif file and without the 'add H-atoms' option during refinement, things work fine,. ) ---------------- AssertionError : Traceback: File "/Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/ cctbx_project/libtbx/thread_utils.py", line 233, in run return_value = self._target(self._args, self._kwargs, self._c) File "/Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/ cctbx_project/libtbx/runtime_utils.py", line 80, in __call__ result = self.target() File "/Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/phenix/ wxGUI2/SimpleApp.py", line 17, in __call__ return self.target(args=list(self.args)) File "/Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/elbow/ elbow/command_line/ready_set.py", line 1038, in run no_file_access=True, File "/Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/elbow/ elbow/command_line/join_cif_files.py", line 151, in run assert 0 ----------------- I have the latest version of Phenix (1.8.1069) and run it on a Mac Book pro (Leopard 10.5.8). Any suggestions please..? Thank you very much Kristof Van Hecke

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phenix.mr_model_preparation_1.8-1069 can't parse hhr
by Dmitry Rodionov 06 Sep '12

06 Sep '12

Dear all, I was trying to run MR_rosetta, but encountered a problem: my hhr files can't be parsed. GUI does not recognize files as HHR and phenix.mr_model_preparation_1.8-1069 exits with the error below. I can't figure out what does it want from me. Any help will be greatly appreciated. Best regards, Dmitry Reading homology search file: local.hhr Sorry: Uninterpretable: 'Q ss_pred CC-CCCeEEEEECCCCcccccCHHHHHHHHHHHHHhCCCcEEEEechHHH------------------------------\nQ Sht1-d52 42 AP-IPQRVWQTWKVGADDKNFPSSFRTYQKTWSGSYSPDYQYSLISDDSI------------------------------ 90 (428)\nQ Consensus 42 ~~-IPk~IwQtW~~~~~~~~lP~~~~~~i~sW~~~~nP~~~~~l~~D~~~------------------------------ 90 (428)\n .+ |||+||.+|.++ .+|+..+.|+.+| ++.+|||++.+|+|.++ \nT Consensus 93 ~~~IPKiIHyIWiGg----~~P~~~~~yI~sW-kk~~PDYei~lW~Dsna~lA~~LKk~i~e~A~~~~~~~~~~~~~d~~ 167 (551)\nT 2vk9_A 93 STIASKNLSFIWIGG----PISDQSLEYYNMW-KMFNKDYNIRLFYDKNSLLVNTLKTAIIQESSKVIIEQNQSNILDGT 167 (551)\nT ss_dssp SCBCCSEEEEECCSS----CCCHHHHHHHHHH-HHHCTTSEEEEEECTTCCCHHHHHHHHHHHHHHHHHHTTSGGGTTTS\nT ss_pred CCCCCcceEEEEcCC----CCCHHHHHHHHHH-HHHCcCCEEEEEeccchHHHHHHHHHHHHHHHHHHHHHHhhccCccc\n\n\nQ ss_pred --------------------------------------HHHHHHhcccChHHHHHHHh----------------------\nQ Sht1-d52 91 --------------------------------------IPFLENLYAPVPIVIQAFKL---------------------- 110 (428)\nQ Consensus 91 --------------------------------------~~~V~~~~~~~Pdv~eay~~---------------------- 110 (428)\n .+|+...++...+.++.|.. \nT Consensus 168 ~~~~~fy~~~l~~i~~~Q~~f~Nyy~~~~~~~s~D~~ri~yL~~~~~~d~eeLe~~k~~n~~ki~~~~g~DIr~l~~f~~ 247 (551)\nT 2vk9_A 168 YGHNKFYSDRMKLIYRYKRELKMLYENMKQNNSVDDIIINFLSNYFKYDIGKLNNQKENNNNKMIAIGATDINTENILTN 247 (551)\nT ss_dssp CCSCTHHHHHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHTCEEGGGTTCSCH\nT ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcCCCchhHHHhhh\n\n\nQ ss_pred -----------cC-chHHHHHHHHHHHHHHcCCEEEecCceee--ccHHHhhccchh-----------------------\nQ Sht1-d52 111 -----------MP-GNILKADFLRYLLLFARGGIYSDMDTMLL--KPIDSWPSQNKS----------------------- 153 (428)\nQ Consensus 111 -----------lp-~~i~kAD~lRyllL~~~GGIY~DiDt~~l--kPi~~wi~~~~~----------------------- 153 (428)\n ++ +.+..||++|+.+|+.+||||+|+|++|- ..+-.-|..... \nT Consensus 248 ~~~~~Y~~e~~~r~N~aaASDi~R~~il~~~GGiY~D~D~lP~~s~~v~k~I~~~~~~~~~~~e~~~Le~I~k~~~li~~ 327 (551)\nT 2vk9_A 248 KLKSYYYQELIQTNNLAAASDILRIAILKKYGGVYCDLDFLPGVNLSLFNDISKPNGMDSNYWEAAIFEAIANEKKLMNN 327 (551)\nT ss_dssp HHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHCEEEECTTCBSCBCGGGGGGSCCCTTCCHHHHHHHHHHHHHHHTTCCSS\nT ss_pred hHHHHHHHHHHhccchHHHHHHHHHHHHHHhCCEEEeccccccccHHHHHHhcCCCcchhhHHHHhHHHHHHHhHhhccC\n\n\nQ ss_pred ----------------------------hhhcccccccccccccccccccccccccCCCceEEEeecCC---Cccccccc\nQ Sht1-d52 154 ----------------------------WLNNIIDLNKPIPYKNSKPSLLSSDEISHQPGLVIGIEADP---DRDDWSEW 202 (428)\nQ Consensus 154 ----------------------------~l~~~~d~~~p~~y~~~~~~~~s~~~~~~~~~lvvGiE~D~---~~~~W~~~ 202 (428)\n .|. +.+-.+-.+..+ -.. |..+\nT Consensus 328 ~~s~~~d~L~~e~k~~L~~i~~~~~~~~iF~--------------------------pl~d~~Vrd~~~il~R~~-~~~G 380 (551)\nT 2vk9_A 328 YPYKYMEQVPSEIKERILSFVRNHDINDLIL--------------------------PLGDIKISQLEILLSRLK-AATG 380 (551)\nT ss_dssp CCCSSSSSSCHHHHHHHHHHHHTSCHHHHBC--------------------------CCCCCBCCTTCCEEEEEE-CTTS\nT ss_pred CcchhhccCCHHHHHHHHHHHhhccchhhcc--------------------------CccccccCchHHHHHHHH-Hhcc\n\n\nQ ss_pred ccccceEEEEEEEecCCCHHHHHHHHHHHHHHHhhhhhccccccccccccccccccccccccccc-----------cccc\nQ Sht1-d52 203 YARRIQFCQWTIQAKPGHPILRELILNITATTLASVQNPGVPVSEMIDPRFEEDYNVNYRHKRRH-----------DETY 271 (428)\nQ Consensus 203 ~~r~~qf~qw~iaA~PgHPvL~~~I~~I~~~~~~~~~~~~~~~~~~~d~~~~~~~n~~~~~~~~~-----------~~~~ 271 (428)\n | +.+.|.+|+|.+|++++..+|..+..+ |+--++. +..|\nT Consensus 381 w---~~~~N~~m~shkgS~~v~~VI~~~~~~---------------------------Y~~l~~~~r~~v~~~~t~~~~f 430 (551)\nT 2vk9_A 381 K---KTFSNAFIISNNDSLTLNNLISQLENR---------------------------YEILNSIIQEKFKICETYDSYI 430 (551)\nT ss_dssp C---EEEEEEEEEECTTCHHHHHHHHHHHHH---------------------------HHHHHHHHHHHHHHCSSHHHHH\nT ss_pred c---cchhhhhHhhCCCCHHHHHHHHHHHHH---------------------------HHHHHHHHHHHHHhhccccHHH\n\n\nQ ss_pred c-------------------------cchhhccccccCCCcccccCcHHHHHHHHHHH\nQ Sht1-d52 272 K-------------------------HSELKNNKNVDGSDIMNWTGPGIFSDIIFEYM 304 (428)\nQ Consensus 272 ~-------------------------~~~~~~~~~~~~~dv~~~TGP~~~Tdai~~yL 304 (428)\n . .+-.+..-..+....+.+|||++++++..++|\nT Consensus 431 ~s~~~~~~e~~~~~~~~~~~~f~~~i~~Y~~Dg~~pe~~~Ti~LtGP~~~~~~~~dl~ 488 (551)\nT 2vk9_A 431 NSVSELVLETTPKNLSMDGSSFYQQIIGYLSSGFKPEVNSTVFFSGPNIYSSATCDTY 488 (551)\nT ss_dssp HHHHHHHHHHSCSSCCHHHHHHHTTGGGSTTBTTBTTCCGGGTTTSHHHHHHHHHHHH\nT ss_pred HhhHHHHHHhccccccccchhHHHHHHHHhhccccccceeeeeccCcHHHHHHHHHHH'

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mr_rosetta and Condor
by Dmitry Rodionov 06 Sep '12

06 Sep '12

Good day! I am trying to get a bunch of OS X 10.6 workstations managed by Condor to work together on an mr_rosetta project. I am new to batch systems and rather confused. The Phenix manual states: "Single file system required for mr_rosetta All files are stored on a single file system that must be accessible to all jobs." What exactly has to go on the network share and how would I make the execution nodes aware of it? Could somebody please share some information on a working setup of this sort? Thanks! Best regards, Dmitry

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phenix/ccp4 monomer library compatibility
by Wulf Blankenfeldt 06 Sep '12

06 Sep '12

Dear all: this may have been asked a thousand times, but: are the ccp4 standard monomer libraries incompatible with phenix.refine, and if yes, is there an easy way to resolve this? I am refining a structure with an FMN, which I build with the "get monomer" option in coot. Unfortunately, phenix.refine doesn't like it and throws it out. Using a cif generated with elbow, on the other hand, has chirality errors (which I can fix...) and isn't liked by coot (0.6.2), which refuses to refine the ligand. Thanks in advance for your help, Wulf -- Prof. Dr. Wulf Blankenfeldt NW-I, 2.0.U1.09 Universitaet Bayreuth fon: +49-(0)921-55-2427 Lehrstuhl fuer Biochemie fax: +49-(0)921-55-2432 Universitaetsstrasse 30 e-mail: wulf.blankenfeldt [at] uni-bayreuth.de 95447 Bayreuth web: www.biochemie.uni-bayreuth.de Germany

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B factor refinement in recent versions of phenix
by "Weiergräber, Oliver H." 31 Aug '12

31 Aug '12

Hello, I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine. The dataset reveals a Wilson B factor of about 23 A². However, if phenix.refine is allowed to run for a number of macrocycles, the mean B value of the model drops continuously to about 9 A². In the end, several atoms are getting values of 0.00! There are no obvious abnormalities in the electron density, and R values are quite good. I was able to dig out an old phenix version (1.7.1) and found that this one behaves perfectly well: mean B around 26 A² (slightly above Wilson B, as is observed frequently) and minimum B around 10 A². So obviously something has happened between versions 1.7.1 and 1.8 ... The latest dev release (1143) shows the same behavior as version 1.8. I should say that this structure is somewhat peculiar (pseudomerohedral twinning plus twofold NCS), but again, the old phenix version handles that without problems. Moreover, the tendency for unreasonably low B factors has been observed recently for a more "conventional" structure in our lab. Any ideas what might be causing this and how to revert to the original behavior? Thanks in advance Oliver ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Kennen Sie schon unsere app? http://www.fz-juelich.de/app

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Phaser and PTNCS - bug fixed in latest builder for Phenix?
by Rafael Lemos Miguez Counago 29 Aug '12

29 Aug '12

Dear all, I noticed on the Phaserwiki webpage (news section) that there is a bugfix (dated 14th of August/2012) for Phaser as the "Packing test was incorrectly applied to reoriented molecules where there was PTNCS". I had a look in the "changes" file, but could not find if this bugfix is part of the latest Phenix installer (dev-1143) or not. Could anybody clarify this point for me? Thanks a lot. Best wishes, Rafael.

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AsCA 12/CRYSTAL 28 Conference and the Bragg Symposium - Early Bird Registration closes this weekend
by John Bruning 29 Aug '12

29 Aug '12

Dear All, Early bird registrations for the Asian Crystallography Association Conference and the Bragg Symposium close this Saturday. You can register for one or both events. **** ** ** The one-day Bragg Symposium on Thursday the 6th of December may be of particular interest as it will specifically address the scientific and historical aspects associated with the centenary of Lawrence Bragg’s explanation of X-ray diffraction. ** ** To register, visit: **** ** ** http://www.sapmea.asn.au/conventions/crystal2012/index.html Kind regards to read this newsletter in your browser click here <http://www.sapmea.asn.au/conventions/crystal2012/emails/enews_01.html>**** [image: cid:[email protected]]**** AsCA 12/CRYSTAL 28 *Conference Newsletter***** Volume 1, May 2012**** Invitation to attend**** *A Joint Meeting of the Asian Crystallographic Association (AsCA), ** Society of Crystallographers in Australia and New Zealand (SCANZ) and the BRAGG Symposium, * November 2012 marks the centenary of the founding of X-ray crystallography by Lawrence Bragg, a field in which he and his father, William, made pre-eminent contributions that were recognised by the award of the Nobel Prize for Physics in 1915. William was the Elder Professor of Physics at the University of Adelaide from 1886 to 1909 and Lawrence was born and educated in Adelaide.**** To celebrate this important anniversary, the legacy of the Braggs’ discoveries in X-ray crystallography and the insights that they have provided into the structure of matter, a combined scientific meeting of the Asian Crystallography Association and the Society of Crystallographers in Australia and New Zealand is to be held in Adelaide from the 2nd to 5th of December 2012. The Conference will be followed by the Bragg Symposium at the University of Adelaide on the 6th of December 2012 that will explore some of the historical context and personal links to the Braggs' work as well as present some of the broader scientific and social impacts of the Braggs' work. The Conference and Symposium will have a strong line-up of national and international speakers.**** Call for Abstracts**** For more information and online abstract submissions please click here: http://www.sapmea.asn.au/conventions/crystal2012/abstracts.html**** Online Registration:**** For more information on online registration and accommodation bookings please click here: http://www.sapmea.asn.au/conventions/crystal2012/rego.html **** **** Conference Secretariat**** [image: cid:[email protected]]**** *sapmea* Unit 12 202 Glen Osmond Rd Fullarton SA 5063 Phone: (08) 8274 6059 Fax: (08) 8274 6000 crystal2012(a)sapmea.asn.au**** ** ** ** **

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Funky message on phaser MR
by Rafael Lemos Miguez Counago 28 Aug '12

28 Aug '12

Dear all, I am getting this message when running Phaser-MR in Phenix (1.8-1069): "Warning: Resolution of data does not achieve (half) expected LLG target: placement of one/first ensemble will be very difficult" The data scales/merges OK. – 99% complete at 2.2A, Rmerge 8.4%. TNCS is detected by Xtriage and Phaser tries to account for that. Coincidently (?) my molecular replacement solution is not looking very good. Any ideas? Best wishes, Rafael.

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HB_score in Ligand Identification
by Brad C. Bennett 24 Aug '12

24 Aug '12

Hello to all- Where can I find a description of what "HB_score" is and how it is calculated in the Ligand Identification program in Phenix? I'm assuming this is a metric for hydrogen bonding capability/propensity of a fit ligand based on distance and angle to model atoms. I have an output rank list of the top 20 ligand fits, ranked by Z-score. The HB_score is all over the place: low = -0.59, high = 77.96, most are between 0-10. I think I understand the correlation coefficient and Z-score but how does the HB_score fit in with these? I can't find this in the documentation or in the Terwilliger et al. (2007) Acta D reference. Somehow I've "lost" the log file, so maybe the information is in there. Thanks in advance! Brad C. Bennett Research Associate- Mark Yeager Lab University of Virginia Molecular Physiology and Biological Physics 320 Snyder Building 480 Ray C. Hunt Drive Charlottesville, VA 22908 Email: bcb3b(a)virginia.edu Lab phone: 434-243-2520

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real space correlation
by Bradley Hintze 23 Aug '12

23 Aug '12

Hey Phenix team, I am trying to get real space correlation measurements for 1eao and ran into a problem. $ phenix.fetch_pdb --mtz 1eao $ phenix.real_space_correlation 1eao.pdb 1eao.mtz Multiple equally suitable arrays of observed xray data found. Possible choices: 1eao.mtz:FOBS,SIGFOBS 1eao.mtz:F(+),SIGF(+),F(-),SIGF(-) Please use .labels to specify an unambiguous substring of the target label. Looking in the options for phenix.real_space_correlation it is unclear how to specify the labels for the reflection file. Any assistance on this would greatly be appreciated. Thanks, Bradley -- Bradley J. Hintze Duke University PhD Candidate Department of Biochemistry Please help me raise money for my ride to assist children with disabilities! <http://www.ridewithoutlimits.org/site/TR?px=1166331&pg=personal&fr_id=1260&…>

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autosol error
by Nora Cronin 22 Aug '12

22 Aug '12

Running phenix.autosol in input wavelength and f" and f' parameters are rejected as follows: "Guessing wavelength for mad is 1.0 Guessing scattering factors for PT at 1.0 A Removing wavelength_list from Facts as length does not match wavelength_list: [1.0721, 1.0538] input_file_list: ['/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_pk_editdname1_PHX_FP_pk.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_pk_editdname1_PHX_F(+)_pk.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_rm_editdname1_PHX_FP_rm.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_rm_editdname1_PHX_F(+)_rm.sca'] NOTE: you may need to select specific datasets from your input files with either group_labels_list (for a script) or peak.labels=xxxx (or similar, for command_line) Removing f_prime_list from Facts as length does not match f_prime_list: [-17.31, -15.31] input_file_list: ['/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_pk_editdname1_PHX_FP_pk.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_pk_editdname1_PHX_F(+)_pk.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_rm_editdname1_PHX_FP_rm.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_rm_editdname1_PHX_F(+)_rm.sca'] NOTE: you may need to select specific datasets from your input files with either group_labels_list (for a script) or peak.labels=xxxx (or similar, for command_line) Removing f_double_prime_list from Facts as length does not match f_double_prime_list: [11.93, 10.5] input_file_list: ['/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_pk_editdname1_PHX_FP_pk.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_pk_editdname1_PHX_F(+)_pk.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_rm_editdname1_PHX_FP_rm.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_rm_editdname1_PHX_F(+)_rm.sca'] NOTE: you may need to select specific datasets from your input files with either group_labels_list (for a script) or peak.labels=xxxx (or similar, for command_line) Why is this rejection of input happening? what does "length does not match" indicate? Best Nora The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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Reproducing a run in phenix.hyss
by Jeffrey, Philip D. 20 Aug '12

20 Aug '12

I've got an interesting potential S-SAD solution that crops up rarely in a script I was using to trawl parameter space in phenix.hyss. Since I was not optimistic of the outcome I did not save all output files. Hyss appears to use a random number generator and allows the seed to be specified on the command line, so is there any way to figure out what random number seed it used based on the information written to stdout while the program is running ? Merely running the command again does not trivially recreate the solution and egrep -i 'rand|seed' LOG only pulls out: Nigel Moriarty, Reetal Pai, Randy Read, Jane Richardson, David Richardson, time_log: p1_recycling random_omit: 990 1.49 0 0.00151 time_log: random_omit: 891 0.62 0 0.000696 Cheers Phil Jeffrey Princeton

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phenix.refine crash
by Maxime Cuypers 18 Aug '12

18 Aug '12

> > Hi, > > i am refining a neutron structure and i keep having this error: > > > File > "/usr/local/phenix-dev-1129/build/intel-linux-2.6/../../phenix/phenix/command_line/refine.py", > line 11, in <module> > command_line.run(command_name="phenix.refine", args=sys.argv[1:]) > File > "/usr/local/phenix-dev-1129/phenix/phenix/refinement/command_line.py", line > 146, in run > call_back_handler=call_back_handler) > File "/usr/local/phenix-dev-1129/phenix/phenix/refinement/driver.py", > line 1533, in run > ncs_manager = self.ncs_manager) > File > "/usr/local/phenix-dev-1129/phenix/phenix/refinement/strategies.py", line > 1109, in refinement_machine > h_params = h_params) > File > "/usr/local/phenix-dev-1129/cctbx_project/mmtbx/refinement/adp_refinement.py", > line 212, in __init__ > nproc = nproc) > File > "/usr/local/phenix-dev-1129/cctbx_project/mmtbx/refinement/adp_refinement.py", > line 315, in __init__ > result = self.try_weight(weight, print_stats=True) > File > "/usr/local/phenix-dev-1129/cctbx_project/mmtbx/refinement/adp_refinement.py", > line 401, in try_weight > minimized = self.minimize() > File > "/usr/local/phenix-dev-1129/cctbx_project/mmtbx/refinement/adp_refinement.py", > line 470, in minimize > self.model.set_refine_individual_adp() > File "/usr/local/phenix-dev-1129/cctbx_project/mmtbx/model.py", line > 1231, in set_refine_individual_adp > iselection = selection_iso.iselection()) > RuntimeError: cctbx Internal Error: > /net/longnose/scratch2/phenix/phenix-dev-1129/cctbx_project/cctbx/xray/scatterer_flags.h(417): > CCTBX_ASSERT(f.use_u_iso()) failure. > > i see the last line is already a known issue as it was already posted in > phenixbb in 2010 but was perhaps solved offline. > > thanks in advance for any help (as i am really stuck) > > -- > Dr. Maxime Cuypers > Institut Laue Langevin (ILL), Deuteration lab > Rue Jules Horowitz, 6, BP 156 > 38042 Grenoble cedex 9 > France > > >

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Real-space and twin refinement
by Haim Rozenberg 13 Aug '12

13 Aug '12

Hello, We've just downloaded and install the new dev-1129 release of phenix hoping to be able to run RS refinement on our twin structures. According to the change log it should be possible with this version. ------------------------------------------------------------------------ Version 1.8.1 and nightly builds (TBA) ====================================== - phenix.refine: - overall B-cart now applied to individual atomic B-factors (restores pre-1.8 behavior) - improvements to torsion NCS rotamer correction - real-space refinement for twinned structures ------------------------------------------------------------------------ Unfortunately, while trying to run - through the GUI - phenix dev-1129 with our twin setting and the "Real space" option, the usual message popped up: "PHENIX error: Real-space refinement is not available for twinned structures." FYI, it runs just fine without the "Real-space" option. Did we have false hopes? Did we misunderstood? Is that a bug? All the best, Haim ============================================ Haim Rozenberg, PhD. Department of Structural Biology Kimmelman Building Weizmann Institute of Science 76100 Rehovot, Israel Phone: +972-8-9344289 FAX:+972-8-9344136 E-Mail: haim.rozenberg(a)weizmann.ac.il<mailto:[email protected]> ============================================ "Quis custodiet ipsos custodes?" D.I. Iuvenalis

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difficult phasing problem
by Ian Slaymaker 10 Aug '12

10 Aug '12

I am trying to solve the structure of a ~30kd monomeric protein for which we have 2.5A diffraction data, and a search model with ~65 % similarity (i have tried, homology models of this and others, as well as using sculpter to build several variations of core search models). I have tried all my possible space groups and a huge range of parameters, and mr_rosetta to rebuild some of my better (but still bad) MR solutions. My LLG is persistently negative (<-1000), which may be due to translational noncrystallographic symmetry which was identified by xtriage. We have unfortunatly been unable to phase this data with selmet SAD, so I am looking for some other MR things to try. Any suggestions for working with tNCS (if this is really the problem) would be much appreciated.

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test set count question
by Filip YABUKARSKI 09 Aug '12

09 Aug '12

Dear all, I am refining a structure with phenix.refine using a .mtz which contains F/SigF and DF/SigDF (CCP format from xdsconv) and i have something like 10000 unique reflections. The test set was created with the uniqueify script. If I understand correctly in the manual it is written that phenix.refine will separate the <F>/<SigF> into "F(+) SIGF(+) F(-) SIGF(-)), instead of keeping the original non-anomalous amplitudes". My question is about the "FREE R VALUE TEST SET COUNT" in the .pdb after phenix.refine. If I understand correctly the number for the test set will also be "doubled" because the <F> will be separated into F+ F-? Logically both F+/F- after separation are kept in the test set is this right? And an impair number for the test set in this case means that only the F+ OR F- was observed? Sorry if I ask a trivial question but I just want to be sure I am using the program in the right way Thanks in advance Filip

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Re: [phenixbb] test set count question
by Kay Diederichs 09 Aug '12

09 Aug '12

Dear Filip, concerning XDSCONV: if FRIEDEL'S_LAW=FALSE, using filetype of CCP4, you get F,SigF,DF,SigDF,isym using filetype CCP4_F, you get F,SigF,F(+),SigF(+),F(-),SigF(-) using filetype CCP4_I, you get IMEAN,SIGIMEAN,I(+),SIGI(+),I(-),SIGI(-) so you can (and should) directly output from xdsconv what you need for a downstream program. A short explanation is at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xdsconv Detailed explanation of each format is at http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xdsconv_formats.h… HTH, Kay

1 0

changing a project directory
by Kendall Nettles 09 Aug '12

09 Aug '12

Dear PHENIX developers, I want to migrate my PHENIX project directories. I moved one project directory as a test, and the GUI doesn't give an opportunity to relocate, which would be a nice feature. Is there a way to edit their location for the PHENIX GUI? Kendall

2 1

two problems about phenix.mr_rosetta
by chen c 08 Aug '12

08 Aug '12

Dear all: I've collected a data set for my crystal, which is a two-protein complex. However, normal molecular replacement method gives no solution and thus didn't work. Right now I'm struglling with the phenix.mr_rosetta method. However, I've got several problems when reviewing it, and thus looking forward to get some advice here. 1: There are such words *"NOTE 2: If your structure contains more than one chain or requires more than one homology model to represent the structure, then you need to use mr_model_preparation and phenix.automr to place your model. Then you can start phenix.mr_rosetta with already_placed=True**"* in phenix documentation page. My understanding for this sentences is: the solution derived from *automr* is treated as an original searching model for phenix.mr_rosetta, in which case, we should add the command line *"run_prerefine=True \ number_of_prerefine_models=1000"*. However, what is *mr_model_preparation * for? And if no solution is given by *automr*, what should I do? What's more important, why not endow the phenix.mr_rosetta program to be capable of dealing with data set from multi-chain protein complexes? Since I thought the idea of preliminary manipulation by the program *automr* would decrease the power of *phenix.mr_rosetta*. 2: Two .hhr files are produced. But as displayed in the phenix.mr_rosetta documentation page, only one .hhr file like *"hhr_files=bfr258e.hhr"* are listed in the command line. Why? Could somebody give me any advice on this, please? Thank you and best regards chen -- Cheng Chen, Ph.D. Candidate Laboratory of Structural Biology Life Science Building,Tsinghua University Beijing 100084 China -

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refining multiple conformations
by Kendall Nettles 08 Aug '12

08 Aug '12

Hi, We have a structure with the ligand showing two overlapping conformers. When we refine it with both conformers separately, it is pretty clear that there are substantial differences in the protein as a result, for about a third of the protein chain. My question is, would it be better to try to define altloc for those specific regions, or would it be OK to refine with two entire alternate protein chains? There is also a second protein chain that shows only a single binding mode for the ligand. It's a 2.0 angstrom structure with 4000 atoms and 27,000 reflections. The yellow map goes with the green model in the attached pic. Also, do we want to let each amino acid have its own occupancy? or should one ligand copy and one chain all have the same occupancy? I'm leaning towards the latter since the differences should be directly tied to the ligand binding mode. Kendall Nettles [cid:[email protected]]

2 1

mr_rosetta problems
by Ian Slaymaker 08 Aug '12

08 Aug '12

I am trying to get mr_rosetta working on our cluster and am running into some problems I am not sure how to solve. The phenix_regression.wizards.test_command_line_rosetta_quick_tests tests went smoothly were completed. However, my first test run with all the defaults (not submitted to multiple processors) using my reflection file, HHR analysis file, sequence file, and the 2 fragment files failed with the below errors. I checked all the files, and it seems this is a problem with the fragment files but I am not sure exactly what they are supposed to look like. I thought it could be because our cluster doesnt have access to any outside networks...is this a problem with rosetta not being able to download pdb files? if so, is there a way to supply them internally? The aligned model looks somewhat what I expected it to (same beta sheet arrangement) but it seems to be incomplete. Any help would be very much appreciated! Splitting work into 100 jobs and running with 1 processors using sh background=None in /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1 Starting job 1...Log will be: /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_1.log ******************* ERROR ENDING *************** mr_rosetta failed... ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_1.log : to match the actual PDB sequence: (protein sequence) New alignment line 4 for PDB: (protein sequence) Start position of target sequence in sequence file: 0 Aligned model for comparison: /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_1/WORK_1/aligned_model.pdb Log for rebuilding: /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_1/WORK_1/rebuild.log **************ERROR ENDING********************** Failed to run REBUILD...see log file in /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_1/WORK_1/rebuild.log The rebuild log had repeats of several errors that I am not sure how to address: core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue PHE 3 (repeated several times) core.fragments.ConstantLengthFragSet: line too short: Skipping line ' (repeated several times) core.fragments.ConstantLengthFragSet: finished reading top 0 0mer fragments from file/dataFiles/aat000_03_05.200_v1_3 protocols.loops.loops_main: Frag libraries debug none 1

4 5

Ordered solvent distances
by Abhinav Kumar 04 Aug '12

04 Aug '12

Hi, The default minimum distance that a water gets placed near protein/water atoms using 'ordered_solvent=true' option in phenix.refine is 1.8. Isn't this too close? Also, if two waters can't get placed in the density due to distance criterion, can phenix place one water in dual conformations in that density? -- Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992

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Lost my job history, can it be recovered? (GUI)
by Andrew Waight 02 Aug '12

02 Aug '12

Hello All, It just so happened that my lab's server ran out of space (someone else uploading datasets) while my phenix rosetta MR job was running. Now the GUI no longer shows any job history in the job history tab (although on the title page the number of jobs is correctly displayed. I cannot find any information on how or if its possible to recover my job history in the GUI. Any tips? Thanks so much. Drew

2 1

July 2012 Computational Crystallography Newsletter
by Nigel Moriarty 01 Aug '12

01 Aug '12

Folks The latest issue of the Computational Crystallography Newsletter is available on-line at http://www.phenix-online.org/newsletter for download. The articles are of general interest to protein crystallographers and are listed below. Enjoy Nigel Moriarty Articles ----------- cctbx tools for transparent job execution on clusters On the analysis of residual density distributions on an absolute scale Short communications -------------------------------- DETAC: tools to detect alternative conformations by unrestrained refinement ERRASER, a powerful new system for correcting RNA models Fitting tips - Rotamer correction with backrub -- Nigel W. Moriarty, PhD Building 64R0246B, 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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what installer would work with a cluster with Darwin 9.8.0 if any?
by Tatyana Sysoeva 28 Jul '12

28 Jul '12

Hi all, I am starting to use a new computer cluster and just found out by uname that it runs Darwin OS? It is totally new to me and I am wondering if Phenix would run on it? should I use just some Mac installer? I would really appreciate any advices! Thank you! Sincerely, Tanya

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Re: [phenixbb] what installer would work with a cluster with Darwin 9.8.0 if any?
by Tatyana Sysoeva 27 Jul '12

27 Jul '12

Thank you Miguel and Ben! I did found the newest release at the cluster after I learned how to use "find" properly! In particular, thank you for pointing out the script to source! Best regards, Tanya

1 0

refinement problem
by Afshan Begum 27 Jul '12

27 Jul '12

Dear Experts I am refining my structures in windows mode and every time i got this crash message i do not know how to solve this issue? If any one encountered this problem kindly suggest me how to solve it. While when i refine with refmac the file proceeds smoothly but i want to refinement in phenix due to utilize some parameters. its end like this: Exporting results ============================== Writing refined structure to PDB file: C:\Documents and Settings\pc user\Desktop\Refine_2\jbu_refine_2.pdb n_use = 7514 n_use_u_both = 7514 n_use_u_iso = 0 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 331 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 7514 After that its not produce the map file and gave errore crash mesage. <module> Bus error (Python call stack above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. Your suggestion highly obliged I would be very thankful to you AFSHAN

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need help
by Afshan Begum 25 Jul '12

25 Jul '12

Dear Experts I am refining my structures in windows mode and every time i got this crash message i do not know how to solve this issue? If any one encountered this problem kindly suggest me how to solve it. While when i refine with refmac the file proceeds smoothly but i want to final refinement in phenix due to utilize some parameters.its end like this: Exporting results ============================== Writing refined structure to PDB file: C:\Documents and Settings\pc user\Desktop\Refine_2\jbu_refine_2.pdb n_use = 7514 n_use_u_both = 7514 n_use_u_iso = 0 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 331 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 7514 After that its not produce the map file and gave errore crash mesage file attached. Your suggestion highly obliged I would be very thankful to you Best Regards AFSHAN

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problem on phenix refine 2
by herohonan 21 Jul '12

21 Jul '12

Hi all: I do not know if someone mentioned this problem here before. Recently I ran the AutoBuild to build the structure model, and it outputs a best model(R/Rfree 0.20/0.24). After that, I tried the program Phenix Refine using the .pdb and .mtz generated by AutoBuild. The R value increased to 0.23/0.30 by the end of this refine. I wonder why this happened? Or if I have done something wrong? (After AutoBuild, I modified the structure and added the substrate moleculars into the structure by hand. I thought the increase of the R value was resulted from the inapposite position of the substrates. But the R value still increased when I ran the Phenix Refine just by inputting the output of the AutoBuild without any manual modification.) -- Tong Huo Ph.D candidate College of Life Sciences Nankai University Tianjin, China

2 1

problem on phenix refine
by 霍彤 20 Jul '12

20 Jul '12

Hi all: I do not know if someone mentioned this problem here before. Recently I ran the AutoBuild to build the structure model, and it outputs a best model(R/Rfree 0.20/0.24). After that, I tried the program Phenix Refine using the .pdb and .mtz generated by AutoBuild. The R value increased to 0.23/0.30 by the end of this refine. I wonder why this happened? Or if I have done something wrong? --

2 1

problems with eLBOW: RuntimeError: Bond distance > max_reasonable_bond_distance: 696.942 > 500:
by Gino Cingolani 19 Jul '12

19 Jul '12

Hi all (Nigel), I'm trying the generate restraints for a large structure that also contains 12 ANPs, 4 ADPa and a a few more ions. When i run "phenix.elbow --do-all MR.1.pdb", phenix crashes with the following... ------------------------------------------------------------------------------ electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.8 1069 - Nigel W. Moriarty (NWMoriarty(a)LBL.Gov) ------------------------------------------------------------------------------ Input format is PDB MoleculeClass : C:20 N:11 O:22 P: 5 (PDB format) 58 atoms 0 bonds 0 angles 0 dihedrals 0 rings Molecule was trimmed MoleculeClass : C:10 N: 6 O:12 P: 3 (PDB format) 31 atoms 0 bonds 0 angles 0 dihedrals 0 rings Predicted memory usage by semi-empirical method : 47Mb Timing estimates Python portion / ATP : 100% c++ optimisation cycle / ATP : 100% Hydrogens may be required to determine the correct bonding 0:05 Hydrogenise Hydrogenise Hydrogenise Hydrogenise Hydrogenise Hydrogenise H Traceback (most recent call last): File "/usr/local/phenix-1.8-1069/build/intel-linux-2.6-x86_64/../../elbow/elbow/command_line/builder.py", line 2240, in <module> run() File "/usr/local/phenix-1.8-1069/build/intel-linux-2.6-x86_64/../../elbow/elbow/command_line/builder.py", line 2038, in run molecule = builder(molecule, options) File "/usr/local/phenix-1.8-1069/build/intel-linux-2.6-x86_64/../../elbow/elbow/command_line/builder.py", line 870, in builder pre_optimise_selections=pre_optimise_selections, File "/usr/local/phenix-1.8-1069/elbow/elbow/utilities/OptimiseMixins.py", line 1009, in ExplodeAndOptimise opt_cycles=1, File "/usr/local/phenix-1.8-1069/elbow/elbow/utilities/OptimiseMixins.py", line 270, in OptimiseSelectedAtoms show_geo=show_geo, File "/usr/local/phenix-1.8-1069/elbow/elbow/utilities/OptimiseMixins.py", line 673, in OptimiseCCTBXProgression additional_restraints=additional_restraints, File "/usr/local/phenix-1.8-1069/elbow/elbow/cctbx_api/CCTBXMixins.py", line 262, in GetNewManager debug=debug, File "/usr/local/phenix-1.8-1069/elbow/elbow/cctbx_api/geometry_manager.py", line 173, in run pair_proxies = manager.pair_proxies(sites_cart=sites_cart) File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/manager.py", line 595, in pair_proxies check_bonded_distance_cutoff(sites_cart=sites_cart) File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/manager.py", line 499, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 696.942 > 500: distance: 1 - 31: 478.879 distance: 2 - 32: 603.994 distance: 5 - 33: 595.912 distance: 7 - 34: 479.110 distance: 13 - 35: 389.539 distance: 13 - 36: 559.710 distance: 14 - 37: 561.219 distance: 16 - 38: 696.942 distance: 17 - 39: 571.138 distance: 18 - 40: 497.529 distance: 19 - 41: 593.584 distance: 20 - 42: 483.447 distance: 22 - 43: 566.195 distance: 26 - 44: 561.483 distance: 26 - 45: 470.865 distance: 28 - 46: 628.947 Any clues? All nucleotides look good by eye. Thanks, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

2 1

Collect MR solution to same ASU?
by Francis E Reyes 18 Jul '12

18 Jul '12

I remember there being a phenix cmd line utility that collects MR solutions to the same asymmetric unit. Or was I dreaming? F --------------------------------------------- Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

2 1

CCP4 6.3.0 released
by ronan.keegan＠stfc.ac.uk 17 Jul '12

17 Jul '12

Dear All, We're very pleased to announce the release of the latest version of the CCP4 Software Suite. Version 6.3.0 (Settle) is now available from the CCP4 download website: http://www.ccp4.ac.uk/download.php The release is available for Linux, Mac OSX and Windows platforms, and delivers a number of new programs, updates and features: 1. New Components and Updates: New: Aimless (Scaling and Merging, replacement for Scala) Prosmart (Generation of external restraints for Refmac) Nautilus (Automatic building of RNA/DNA) Ample (Automatic Ab initio modelling for Molecular Replacement) Dimple (Automatic difference map calculation) Zanuda (Space group checker/validator) CMapCut (Preparation of electron-density search model for MR) Comit (Composite omit maps) Gesamt (Structure aligner not using secondary structure assignments) ViewHKL (Graphical viewer for reflection data) Updated: Mosflm v7.0.9 (Data processing/reduction) iMosflm v1.0.7 (Mosflm GUI) Pointless v1.6 (Laue group determination) Refmac v5.7 (Macromolecular refinement) Phaser v2.5.1 (Molecular Replacement and Experimental Phasing) MrBump (Automatic Molecular Replacement, now includes phaser.sculptor models) Xia2 (Automated data reduction) CCP4mg v2.6.2 (CCP4 Molecular Graphics, much improved on features and stability) CCP4 Graphical User Interface: - new automation module - provides interfaces for new and updated modules - ViewHKL option for viewing reflection (mtz) files More information on updates is available from: http://www.ccp4.ac.uk/html/CHANGESinV6_3.html 2. ARP/wARP co-distribution Release 6.3.0 marks a milestone in collaboration between CCP4 and ARP/wARP teams by releasing ARP/wARP Model Building software v7.3 jointly with CCP4 Software Suite. In order to get ARP/wARP Software, academic users need only to select the appropriate package from download pages or with our new Package Manager, and type in their name and e-mail address where required. Commerical users will be required also to provide their reference number, obtainable separately from EMBL-EM. ARP/wARP 7.3 includes the following major updates and changes (on behalf of Victor Lamzin): - The protocols for the use of NCS in protein chain tracing have been improved and expanded to a wider range of resolutions. - Common ligands can now be automatically identified and fit into a specified electron density. - The algorithm for modelling partial ligands (cocktail screening) has been replaced with a new one that applies a number of sophisticated numerical features - The ARP/wARP graphics front-end, ArpNavigator, automatically assigns secondary structure and has an improved visual presentation of a static model or real time protein or ligand building. - Supported computer platforms are Mac powerpc, Mac Intel and Linux (including 32 and 64-bit versions). - The ARP/wARP installer has been considerably updated on all platforms. - Joint software release and authentication with the CCP4 is now possible. - CCP4 6.3.0 and Refmac 5.7.0029 are the recommended versions to use with ARP/wARP 7.3. 3. 64-bit precompiled packages Starting with version 6.3.0, CCP4 distributes both 32-bit and 64-bit precompiled binaries for Linux. Note that 64-bit codes will not run on 32-bit architectures, and 32-bit codes will run on 64-bit setups only if 32-bit libraries are installed (not a default for most Linuxes). THEREFORE: PLEASE MAKE SURE THAT YOU HAVE SET THE 32-bit/64-bit SWITCH ON TOP OF THE DOWNLOAD PAGES CORRECTLY BEFORE ALL! 4. "Friendly" Coot and CCP4mg distributions Coot is known to be less portable than the rest of CCP4 Program Suite. CCP4mg is more portable and requires special builds only for older Linuxes. Our new Package Manager will try to automatically choose Coot and CCP4mg bundles that are most appropriate for your system. In addition, our new download pages will offer you a range of precompiled Coot and CCP4mg packages, from where you may choose ones that work for you. 5. New distribution mechanism We hope that you will find our new Download Pages more intuitive and convenient than before. We have worked hard to improve our Windows installer, to make it working faster and smoother. On Linux and Mac platforms, we recommend using Package Manager, a small graphical application that allows you to select the desired components, and automatically download and install them on your system. Note that Package Manager features resumable downloads, which may be useful for users with slow or less reliable Internet connection. We would like to thank all of the developers who have contributed into CCP4 6.3.0, and all of those who have helped in testing it. The following publication should be used to cite the use of CCP4: M. D. Winn, C. C. Ballard, K. D. Cowtan, E. J. Dodson, P. Emsley, P. R. Evans, R. M. Keegan, E. B. Krissinel, A. G. W. Leslie, A. McCoy, S. J. McNicholas, G. N. Murshudov, N. S. Pannu, E. A. Potterton, H. R. Powell, R. J. Read, A. Vagin and K. S. Wilson (2011) Overview of the CCP4 suite and current developments, Acta Cryst D67 235-242. CCP4 is supported by the BBSRC UK through grant BB/F0202281, as well as by the number of industrial users. CCP4 6.3.0 is out now, and we hope that you will find it a helpful advance in crystallographic computing. Best wishes, CCP4 Core Team -- Scanned by iCritical.

1 0

Van der waals interaction in phenix
by subhash bihani 16 Jul '12

16 Jul '12

Hi all, In one of my structure I have to put some water molecule in alternate confimation with amino acid residues and in another case with ligand. How do I do it in Phenix. Regards -- Subhash Bihani Scientific Officer Solid State Physics Division Bhabha Atomic Research Centre Trombay, Mumbai-85 Ph. 25594688 (o) alternate email: subhashbihani(a)yahoo.co.in

3 2

default treatment of Intensities and structure factors in phenix.refine
by Yarrow Madrona 16 Jul '12

16 Jul '12

Hi, I recently noticed from reviewing the phenix.refine log file that phenix is scaling the input intensities using the French-Wilson Method. However, I have already run Truncate in CCP4 and have structure factors in my MTZ. So it appears that Phenix.refine ignores structure factors and uses intensities regardless. The reason I am concerned is that Nat recently mentioned that the default for the sigma I cutoff is zero. However, The default in Truncate I thought was -3. If I understand correctly, the treatment in truncate allows weak reflections to be scaled and converted to structure factors. It seems that setting the I sigma cutoff to zero would cause you to loose some useable data. Currently, the sigma_fobs_rejection_criterion and sigma_ibos_rejection_criterion = None. This is the default I guess which would be 0. So my questions are: 1. Will setting: sigma_iobs_rejection_criterion = -3 result in Phenix using a sigma I cutoff of -3? 2. How do I tell phenix to use the structure factors created by Truncate? Thanks for your help. I apologize if I have some misconceptions as I am still relatively new to crystallography. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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average temperature factor
by Ursula Schulze-Gahmen 15 Jul '12

15 Jul '12

Is there an easy way to calculate average temperature factors in phenix or another program after ADP + TLS refinement in phenix? Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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output of labelit.check_pdb_symmetry
by "Weiergräber, Oliver H." 15 Jul '12

15 Jul '12

Hello, I am using labelit.check_pdb_symmetry in order to evaluate a crystal structure with sg P21 (2 copies/asu) and all angles indistinguishable from 90 degs for potential higher (i.e. orthorhombic) symmetry. Comparison of refinement statistics clearly indicates that the most likely scenario is perfect pseudomerohedral twinning of a true P21 crystal (Rfree=0.21). Accordingly, labelit.check_pdb_symmetry reports a striking discrepancy between Rsymop(Iobs) and Rsymop(Icalc): 8 % vs 31 %, i.e. there is an additional (apparent) 2-fold symmetry in the data which cannot be explained by the model. In an attempt to force a solution for comparison and visualization purposes, I have increased the r_symop_tol parameter to 0.35; the program starts to evaluate possible space groups with fTF, yielding scores (these are correlation coefficients, right?) way above 90 %. Still, in the end it reports there are no higher symmetry solutions. Why is this? Does the program check for the contrast between the best solution and the others? Changing peak_cutoff to a "discriminative" value did not help... Best regards, Oliver ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Kennen Sie schon unseren neuen Film? http://www.fz-juelich.de/film Kennen Sie schon unsere app? http://www.fz-juelich.de/app

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Re: [phenixbb] phenixbb Digest, Vol 80, Issue 6
by Yuri 14 Jul '12

14 Jul '12

On Fri, 13 Jul 2012 12:13:15 -0700, phenixbb-request(a)phenix-online.org wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Re: segmented rigid body refinement (Nathaniel Echols) > 2. Re: segmented rigid body refinement (Pavel Afonine) > 3. Re: average temperature factor (David Cobessi) > 4. Re: segmented rigid body refinement (Gino Cingolani) > 5. Re: average temperature factor (Pavel Afonine) > 6. Re: output of labelit.check_pdb_symmetry (Nicholas Sauter) > 7. Re: average temperature factor (Nathaniel Echols) > > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 12 Jul 2012 09:40:41 -0700 > From: Nathaniel Echols <nechols(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] segmented rigid body refinement > Message-ID: > <CALeAa1NE=F6Quwvsm=ijGf_j-QMxwN1KqStpwiE6NJ7bmyKnsw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > On Thu, Jul 12, 2012 at 9:33 AM, Gino Cingolani < > Gino.Cingolani(a)jefferson.edu> wrote: > >> The latter....something more analytical to split individual chains >> into >> smaller groups >> (e.g. like to define tls groups). >> > > Airlie McCoy just added some functionality to do this in Phaser using > normal mode analysis. It is still somewhat experimental and in flux > (i.e. > the program name isn't even finalized), but I will email you off-list > with > details. > > -Nat >

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segmented rigid body refinement
by Gino Cingolani 13 Jul '12

13 Jul '12

Hi all, I'm refining a large oligomeric structure at low res (~6A). I'd like to define groups to use for 'segmented rigid body refinement'. Is there any rational way to define 'segments'? My macromolecule is already an oligomer on its own, so, intuitively, each protomer is a segment. Thanks, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Nathaniel Echols [nechols(a)lbl.gov] Sent: Thursday, July 12, 2012 7:44 AM To: PHENIX user mailing list Subject: Re: [phenixbb] RFZ is higher than TFZ On Thu, Jul 12, 2012 at 12:38 AM, 周文昌 <wenchangyu2006(a)gmail.com> wrote: > I had one problem using phaser-MR to solve my structure. Phaser-MR gives me > one solution with TFZ=15.4 and LLG=165 which seems to be promising but > phenix.refine does not give me a low R values (0.4884/0.5424). I went back > and checked the solution from phaser-MR, I found RFZ=18.8, higher than TFZ. > Does anyone think this is a problem to solve my structure? > > The space group is C121, I believe there are 4 copies of my search model in > ASU. What is the resolution, and what is the sequence identity of the search model? I don't know whether the high RFZ means anything, but the first thing I would check is whether the packing of the MR solution makes sense; Phaser will do a good job preventing molecules from overlapping (unless you changed it to use much less conservative criteria), but it won't guarantee that the molecules pack into a nice continuous lattice. If there are big gaps, it may not be a real solution. I think we need to add an entire FAQ page for high R-factors. However, there are an increasing number of tools and/or tricks in Phenix to deal with problems like this - in approximate order of runtime: - run phenix.refine for more cycles - at least 20. See this paper for an example of why this can be important: http://journals.iucr.org/d/issues/2012/07/00/kw5044/index.html - use phenix.morph_model (refer to previously mentioned paper) - use phenix.den_refine (or DEN in CNS) - use MR-Rosetta Also, if you're willing to share your data with us, we're collecting difficult-to-refine structures for benchmarking new methods. (It will of course be kept confidential.) -Nat _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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v1.8 bug ? memory allocation crash in map calculation (phenix.refine, phenix.maps)
by Phil Jeffrey 13 Jul '12

13 Jul '12

This is in F432 in a=b=c=340A at 2.85A resolution. Mac OSX 10.5.8, the machine has 8Gb memory of which something like 6Gb is hanging around begging to be used. 1,327,104,000 if that's in bytes doesn't seem all that excessive. On the other hand, 340*340*340= 39,419,600 so it's perhaps a little greedy. Limits set by shell: phil% limit cputime unlimited filesize unlimited datasize unlimited stacksize 65532 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 266 phenix.refine does the same thing right at the end, which is kind of a shame since it takes quite a long time to run. phenix.maps does the same thing even if I ask it just to generate F,phase in MTZ format. [snip] Compute maps. Python(632) malloc: *** mmap(size=1327104000) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug show_stack(1): /usr/local/phenix-1.8-1069/cctbx_project/cctbx/miller/__init__.py(3067) double_step_filtration show_stack(2): /usr/local/phenix-1.8-1069/cctbx_project/mmtbx/maps/__init__.py(416) map_coefficients_from_fmodel show_stack(3): /usr/local/phenix-1.8-1069/cctbx_project/mmtbx/maps/__init__.py(543) __init__ show_stack(4): /usr/local/phenix-1.8-1069/build/mac-intel-osx/../../cctbx_project/mmtbx/command_line/maps.py(325) run show_stack(5): /usr/local/phenix-1.8-1069/build/mac-intel-osx/../../cctbx_project/mmtbx/command_line/maps.py(402) <module> Bus error (Python call stack above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical.

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RFZ is higher than TFZ
by 周文昌 12 Jul '12

12 Jul '12

Dear all, I had one problem using phaser-MR to solve my structure. Phaser-MR gives me one solution with TFZ=15.4 and LLG=165 which seems to be promising but phenix.refine does not give me a low R values (0.4884/0.5424). I went back and checked the solution from phaser-MR, I found RFZ=18.8, higher than TFZ. Does anyone think this is a problem to solve my structure? The space group is C121, I believe there are 4 copies of my search model in ASU. thanks, Wenchang

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sigma_iobs_rejection_criterion
by Yarrow Madrona 11 Jul '12

11 Jul '12

Hello, I am refining a structure using a.eff file that I generated in Phenix version 1.7 GUI and later ran in the command line. When I try to run the same refinement in Phenix V.1.8 I get the following error: For French and Wilson scaling, sigma_iobs_rejection_criterion must be set between -4.0 and -1.0 I see that it was set to zero previously. My questions are: 1. Is this the same observed criterion that is reported in the RCSB Deposition? 2. To be honest I don't understand what this is. Is it a limit for the error in Iobs, below which the reflection will be discarded? 3. What is a reasonable setting for this input and how does it change the refinement? Thank you (I appreciate your help as I know these may be very basic questions). -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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Phenix autosol error 2L MAD
by Graeme Winter 10 Jul '12

10 Jul '12

Hi Folks, 2L MAD data set where SHELXC/D/E works fine I (repeatedly) get this error, through GUI or scripts... resolution: 1.7 recommended_resolution: 1.9 datafile_for_hyss: /Users/graeme/projects/test/12287_build/AutoSol_run_10_/TEMP0/ANISO_subset_PHX_I(+)_WAVE1.sca_ano_1.sca aniso_corrected: True aniso_b_min: 13.2 aniso_range_of_b: 6.8 RUNNING HYSS on ANISO_subset_PHX_I(+)_WAVE1.sca_ano_1.sca from PDS as miller arrays *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoSol_hyss: HYSS failed...Probably no iso or ano differences... ******************************************************************************** *************ERROR ENDING ******************* The data set works fine with a third (radiation damaged) data set. There is also a massive anomalous signal in the data (2L) as it stands. here's the PHIL: autosol { seq_file = 12287.seq sites = 8 atom_type = Se crystal_info { unit_cell = 51.59 51.59 157.69 90 90 90 space_group = "P 43 21 2" solvent_fraction = 0.52 chain_type = PROTEIN resolution = 0 change_sg = True } wavelength { data = subset.mtz lambda = 0.97966 f_prime = -9.9 f_double_prime = 3.9 labels = 'I(+)_WAVE1 SIGI(+)_WAVE1 I(-)_WAVE1 SIGI(-)_WAVE1' } wavelength { data = subset.mtz lambda = 1.00000 f_prime = -3.3 f_double_prime = 0.5 labels = 'I(+)_WAVE2 SIGI(+)_WAVE2 I(-)_WAVE2 SIGI(-)_WAVE2' } } Have I done something wrong? Thanks, Graeme

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special position
by Karolina Michalska 10 Jul '12

10 Jul '12

Hi all, I'm refining a structure with a phosphate ion on a 3-fold axis. I set occupancy manually to 0.33 and after refinement the ion has huge B-factor (close to 100) and there is a lot of positive electron density. I found somewhere that phenix recognizes special positions and there is not need to adjust occupancy manually. so I set it to 1 again and re-refined. This time my phosphate sits in a mixture of negative and positive density with B factor around 90 (for comparison Refmac refines it to ~20). Now I'm confused which procedure to follow. Karolina

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I/O error in writing very large B-factors
by Phil Jeffrey 10 Jul '12

10 Jul '12

This occurs at the end of refinement. Quite why it's trying to *read* from a string with Fortran-esque overflow formatting while in a writing step I don't know, but the PDB file gets truncated at REMARK IF THIS FILE IS FOR PDB DEPOSITION: REMOVE ALL FROM THIS LINE UP. The structure is not idyllic, clearly, but I'd like to see the extent of the problem rather than just the first atom. Got to be pretty easy to trap for and map to 999.99 either on the way in or out. Writing refined structure to PDB file: /Users/phil/Structures/reference_models/start_refine_001.pdb n_use = 21264 n_use_u_iso = 21264 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 21264 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 21264 Traceback (most recent call last): File "/usr/local/phenix-1.7.3-928/build/mac-intel-osx/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.7.3-928/phenix/phenix/refinement/command_line.py", line 105, in run refine_object.write_refined_pdb(f_pdb) File "/usr/local/phenix-1.7.3-928/phenix/phenix/refinement/driver.py", line 1379, in write_refined_pdb ignore_hd = not self.neutron_refinement) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model_statistics.py", line 589, in __init__ ignore_hd = ignore_hd) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model_statistics.py", line 504, in __init__ molprobity_scores=True) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model.py", line 1063, in geometry_statistics molprobity_scores = molprobity_scores) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model_statistics.py", line 112, in __init__ self.clashscore_obj.analyze_clashes(hierarchy = pdb_hierarchy) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/validation/clashscore.py", line 182, in analyze_clashes self.pdb_hierarchy = pdb.hierarchy.input(pdb_string=input_str).hierarchy File "/usr/local/phenix-1.7.3-928/cctbx_project/iotbx/pdb/hierarchy.py", line 1044, in __init__ source_info=source_info, lines=flex.split_lines(pdb_string)) File "/usr/local/phenix-1.7.3-928/cctbx_project/iotbx/pdb/__init__.py", line 582, in input return ext.input(source_info=source_info, lines=lines) ValueError: string, line 5148: ATOM 17 N ILE A 268 -16.878 -22.262 49.415 1.00****** A N ------------------------------------------------------------^ not a floating-point number. Phil Jeffrey Princeton

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Iridium hexamine problems with eLBOW
by Benoît Masquida 08 Jul '12

08 Jul '12

I experience problems generating a correct CIF file for iridium hexamine (IRI in the eLBOW database). The geometry is supposed to be octahedral and eLBOW outputs a prism regardless of the options checked in the GUI. eLBOW actually does the same for the octahedral Mg(OH2)6. Does someone know how to rule this out? Thanks to everybody. Ben -- Benoît Masquida Chargé de Recherche CNRS IBMC Strasbourg UPR 9002 ARN b.masquida(a)ibmc-cnrs.unistra.fr +33 (0)3 88 41 70 45 +33 (0)6 70 23 79 50 +33(0)3 88 60 22 18 (fax)

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Subject: no kidding - we need small crystals!
by jens j birktoft 06 Jul '12

06 Jul '12

Hi everybody, Any suggestions regarding how to generate small!! crystals? Yes, in this case that is what we want While we can generate crystals of size 100-500 microns, this time we something in the range of .5-5 microns. Any ideas and suggestions would be greatly appreciated, Cheers Jens

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ask refinement question including an aligo as the ligand
by crystallogrphy 05 Jul '12

05 Jul '12

Hi, I want to refine my structure including a sugar oligomer as the ligand in Phenix GUI. I first put each subunit into the density and merge them together as the oligomer in Coot. Then I merged the oligomer coordinates to the protein file. Then I run phenix.elbow to get the cif file. Finally, I run phenix.refine. However, the oligomer units were pushed away from each other. I guess I need to modify the cif file to link the oligo units together. Does anyone know how I can I do it? thanks!

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Re: [phenixbb] phenixbb Digest, Vol 80, Issue 1
by Matthew J. Whitley 05 Jul '12

05 Jul '12

Hello, One simple thing that might be the problem: As I'm sure you know, oligosaccharides are formed via intermolecular dehydration reactions. If I understand you correctly, you built the oligosaccharide by loading the component monomers into the density in Coot and then joined them together. Whenever two sugars are joined together, three atoms are given off as a water molecule. Did you actually delete the appropriate oxygen and two hydrogens from your coordinates for each glycosidic linkage in your structure? If you didn't, then it doesn't matter whether you told Coot or Phenix that the monomers or linked, you'll still have atoms trying to occupy the same space and thus the refinement will blow them apart. Not that I have EVER made that mistake myself . . . Similar topics have come up on the Phenix BB before. For other possibly useful information, see: http://phenix-online.org/pipermail/phenixbb/2012-April/018390.html http://www.phenix-online.org/pipermail/phenixbb/2009-October/013951.html Good luck! Matthew --- Matthew J. Whitley, Ph.D. Postdoctoral Research Fellow Angela Gronenborn Lab Department of Structural Biology University of Pittsburgh School of Medicine On Wed, July 4, 2012 7:55 pm, phenixbb-request(a)phenix-online.org wrote: > > > Message: 14 > Date: Wed, 4 Jul 2012 15:28:09 -0400 > From: crystallogrphy <qunwan1(a)gmail.com> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] ask refinement question including an aligo as the > ligand > Message-ID: > <CANcEHNi95ss+Tst8+8JVTK3=B598HjC_NNg5N7_=6-whdMTXpQ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I want to refine my structure including a sugar oligomer as the ligand in > Phenix GUI. > > I first put each subunit into the density and merge them together as the > oligomer in Coot. Then I merged the oligomer coordinates to the protein > file. Then I run phenix.elbow to get the cif file. Finally, I run > phenix.refine. However, the oligomer units were pushed away from each > other. I guess I need to modify the cif file to link the oligo units > together. Does anyone know how I can I do it? > > thanks!

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