- phenixbb - phenix-online.org

Autosol: MIRAS
by ash.k＠aol.com 06 Sep '12

06 Sep '12

Hi all, I am tryingto solve a structure through experimental phasing using AUTOSOL. I have acouple of heavy atom derivative datasets (Hg, La, Eu, Cd) and also a SeMetdata. Unfortunately all the datasets are of low resolution (3.7-4.2A) and thereare possibly 4-8 molecules in the asu. MIR, SAD and MAD alone did not give any convincing solution. However,MIRAS, with a combination of few heavy atom datasets and the anomalous datafrom SeMet crystals, gave a somewhat satisfactory map. But the heavy atom sitepicked by AUTOSOL list only one of the heavy atoms i.e. Lanthanum. In another set of run, the solution of which was not convincing, the heavy atom substructure had only Hg. There are 6Met out of 200 residues in one molecule and mass spec results show that Seincorporation is 100%. Now, mydoubt is that why does the heavy atom substructure contain only La and how canI get the substructure involving Se from this solution (or the datasets used)? Se location is going to help me a lot forfinding a starting point to assign side chains. Anysuggestion would be greatly appreciated. Thanks AK

4 8

Partially occupied side chains in special position
by Nicholas Keep 05 Sep '12

05 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

2 1

Adding H atoms - AssertionError
by Kristof Van Hecke 05 Sep '12

05 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

5 6

phenix.mr_model_preparation_1.8-1069 can't parse hhr
by Dmitry Rodionov 05 Sep '12

05 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'

2 3

mr_rosetta and Condor
by Dmitry Rodionov 05 Sep '12

05 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

2 3

phenix/ccp4 monomer library compatibility
by Wulf Blankenfeldt 05 Sep '12

05 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

5 4

B factor refinement in recent versions of phenix
by "Weiergräber, Oliver H." 30 Aug '12

30 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

4 5

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.

3 3

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

28 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**** ** ** ** **

1 0

Funky message on phaser MR
by Rafael Lemos Miguez Counago 27 Aug '12

27 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.

3 4