June 2015 - phenixbb - phenix-online.org

mmCIF file must contain at least one data block
by Ursula Schulze-Gahmen 18 Dec '15

18 Dec '15

I am getting this thie error message mmCIF file must contain at least one data block when trying to run readyset or phenixrefine I cannot find anything wrong wqith my input files. What is the problem? Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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labelit distl_minimum_number_spots_for_indexing
by Christian Roth 21 Sep '15

21 Sep '15

Dear Phenix-Team I installed the latest nightly build 1.8-1069. I tried to index some diffraction images and to overwrite the minimum usable spots for indesing I tried the suggested command. However If I try this command, it seems that it does not exist. At least in the list of the possible distl commands it does not show up. Do I have to install some additional stuff or change some preferences to get this command? Best Regards Christian

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Refinement with new mtz.file
by Aleksandar Bijelic 14 Jul '15

14 Jul '15

Dear CCP4 user and experts, I refined (with PHENIX) a 3.0 A dataset obtaining Rfree of about 0.24 (with good geometry according to Ramachandran, Beta Outliers, etc.) .... Everything seems to be ok (especially in relation to the resolution) .... because the mtz.file I used was quite old and I cannot find my xscale.hkl file, I processed the data set again (this time with optimizng and polishing) and received a "better" file according to almost everything (resolution limit, I/sigma, CC(1/2), Rmeas), thus I used this new mtz.file and put it in my last refinement step (the refinement which led to the above mentioned Rfree = 0.24). Suprisingly, the refinement starts at Rwork = 0.18 and Rfree = 0.19 but ending up with 0.20 and 0.22, respectively. So I wanted to know if this is usual? I was expecting my data to become slightlly better but what is irritating me is the starting R-values of the refinement and that it get worse during refinement. Maybe I did something wrong? Is it reasonable to replace the mtz.file with a new one in the last refinement step or should I start the refinement from the scratch? In the sake of completeness, I deleted the header of the used pdb.file because of the R-flag error which occurs, since Phenix reconizes that the pdb.file was already used with other Rflags. Sorry, but I am still a beginner in this field, so I would be very grateful if somebody could explain me this situation and my mistake and if I need to start refinement from the beginning. Thank you in advance! Best Regards. Aleksandar -- ------------------------------------------- Aleksandar Bijelic, MSc. Institut für Biophysikalische Chemie Universität Wien Althanstrasse 14 A-1090 Wien Tel: +43 1 4277 52536 e-Mail: aleksandar.bijelic(a)univie.ac.at --------------------------------------------

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phenix rosetta refine
by Jens Kaiser 06 Jul '15

06 Jul '15

Hey there, who would be the person to talk about setting up phenix.rosetta_refine? I tried our SBgrid installation with overrides to "nightly" for phenix and rosetta; I tried a clean install of rosetta and phenix - production version and nightly's in all combinations - and all combinations of compiling (rosetta first, then rosetta.build_phenix_interface, phenix first, then rosetta.build_phenix_interface). The problem is that "phenix.rosetta_refine" seems to run, and produce a log file that looks reasonable, but geometry params are worse than with an ordinary refine. I think I tracked it down to the fact that the "rosetta_XX.sh" files are empty, and rosetta actually does not run. Any help is welcome - and any support will be extended. Cheers, Jens

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labelit access in Phenix?
by Keller, Jacob 03 Jul '15

03 Jul '15

Dear Phenix list, Does anyone know how to access labelit through Phenix to determine whether the highest possible symmetry has been found? I exclusively use the GUI, and it's on win7. In the labelit documentation/homepage it mentions the command: labelit.check_pdb_symmetry [pdb coordinate file] [data=mtz file] But I did not find any executables called labelit, nor can I figure out how to run Phenix from command line in Win7, short of installing Cygwin or something. JPK

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C-beta RMSD
by Kaushik Hatti 02 Jul '15

02 Jul '15

Hi, Is there a tool which can calculate C-beta RMSD for equivalent amino acids of homologous structures, post C-alpha superposition? Sorry if its off topic, Thanks, Kaushik -- Stupidity is everyone’s birthright. However, only the learned exercise it! --Kaushik (28Oct2014)

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Simulated annealing refinement for just one domain
by Appu kumar 30 Jun '15

30 Jun '15

Hello All, I was wondering if there is a simulated annealing refinement for the just one domain and keeping the other domain fix. I have a structure where the electron density is poorly defined which could be because of the some conformation of domain is different. Although the resolution of the data is 4A but channel has well defined density in the TM domain. Thanks in advance for your advice and suggestions. Appu

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while doing tar xvzf of nightly build 1.10pre-2089
by Murpholino Peligro 29 Jun '15

29 Jun '15

I get an error >>>> gzip: stdin: unexpected end of file phenix-installer-1.10pre-2089-intel-linux-2.6-x86_64-centos5/modules/phenix_regression/wizards/command_line_rosetta_tests/test_mr_rosetta_ncs.tgz tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now <<<< Should I try another version?

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Re: [phenixbb] labelit access in Phenix?
by R.D. Oeffner 28 Jun '15

28 Jun '15

This should have been forward to the mailing list. Rob -------- Original Message -------- Subject: Re: [phenixbb] labelit access in Phenix? Date: 2015-06-26 21:46 From: "R.D. Oeffner" <rdo20(a)cam.ac.uk> To: "Keller, Jacob" <kellerj(a)janelia.hhmi.org> Copy: Aaron Brewster <asbrewster(a)lbl.gov>, Nigel W Moriarty <NWMoriarty(a)lbl.gov> Hi Jacob, Labelit is not present on Windows in the last official release of Phenix from May last year, version 1.9-1692. But it is present in recent pre-releases of Phenix as command line tools. When you install Phenix on Windows a startup group is created that includes a command line prompt which recognises Phenix commands. From there you can execute all labelit command line tools. I think Nigel is about to put the recent Windows pre-release online on the Phenix website. Feel free to get in touch with further questions. Regards, Rob On 2015-06-26 18:44, Aaron Brewster wrote: > Hi Jacob, replying off of the list for now. There is no labelit gui > support in the phenix gui. There may be a batch script you have to > run to get the phenix command line binaries in the path for the cmd > program in win7, but I don't know it. If you can run phenix.refine on > the command line but not labelit, that would be instructive. > > cc'ing Rob who has been working on the phenix windows build. > > -Aaron > > On Thu, Jun 25, 2015 at 7:58 PM, Keller, Jacob > <kellerj(a)janelia.hhmi.org> wrote: > >> Dear Phenix list, >> >> Does anyone know how to access labelit through Phenix to determine >> whether the highest possible symmetry has been found? I exclusively >> use the GUI, and it's on win7. >> >> In the labelit documentation/homepage it mentions the command: >> >> labelit.check_pdb_symmetry [pdb coordinate file] [data=mtz file] >> >> But I did not find any executables called labelit, nor can I figure >> out how to run Phenix from command line in Win7, short of installing >> Cygwin or something. >> >> JPK >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb [1] >> Unsubscribe: phenixbb-leave(a)phenix-online.org > > > > Links: > ------ > [1] http://phenix-online.org/mailman/listinfo/phenixbb

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phenix-1.9-1692 pymol problem
by ChenWeiFei 26 Jun '15

26 Jun '15

Dear all, I just install phenix and I found phenix-1.9-1692/pymol/install and it says: INSTALLATION of the PyMOL Executable Build for Unix 1) Extract the appropriate archive. tar -zxvf pymol-0_99-bin-linux-x86-glibc23.tgz 2) Change directory into the root level of the archive. cd pymol 3) Run "./setup.sh" which will create "./pymol" with a record of the current working directory. ./setup.sh 4) Link or copy ./pymol into a directory that is in your path. ln -s `pwd`/pymol /usr/local/bin/pymol (or perhaps) cp pymol /usr/local/bin/pymol 5) Now try it! ./pymol I follow it and when I type pymol there comes an error: $ pymol /usr/local/bin/pymol: /usr/local/phenix-1.9-1692/pymol/pymol.exe: /lib/ld-linux.so.2: bad ELF interpreter: No such file or directory Is any one konw how to deal with it? Best, Weifei

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