Hi Garib, I tried with refmac 5.6 and the same inputs; it worked fine.
Thanks, Lionel 2010/9/6 Garib N Murshudov <[email protected]> > Could you please try refmac 5.6. I think we have fixed this problem. It is > available from: > > www.ysbl.york.ac.uk/refmac/latest_refmac.html > > You need to take experimental version (it is now fairly stable) > > Regards > Garib > > On 6 Sep 2010, at 15:01, Lionel Costenaro wrote: > > > Hello, > > > > When I run Refmac with the mixed iso/anisotripic B-value option (refi > bref MIXED), refmac failed with the error message below. > > My pdb comes from previous refmac runs with anisotropic B values for all > atoms (H generated but not written). > > I just removed from the pdb the ANISOU lines for all water molecules. > > > > Refmac with "refi bref ANIS" (all anisotropic B) works fine (normal > termination) with the same input data and pdb - with all ANISOU lines. > > CCP4Interface 2.0.5 > > Refmac_5.5.0102 > > > > Any comments, help, fix are welcome. > > > > Best regards, > > Lionel > > > > ****************** > > CGMAT cycle number = 1 > > > > ..... > > Trying gamma equal 0.000000 > > Not converging with gamma equal 0.000000 > > Trying gamma equal 5.5000003E-02 > > Not converging with gamma equal 5.5000003E-02 > > Trying gamma equal 0.1155000 > > ..... > > Not converging with gamma equal 2655.967 > > Trying gamma equal 2921.619 > > Not converging with gamma equal 2921.619 > > Trying gamma equal 3213.836 > > Gamma decreased to 3155.393 > > > *************************************************************************** > > * Information from CCP4Interface script > > > *************************************************************************** > > The program run with command: /all/programas/ccp4-6.1.2/bin/refmac5 XYZIN > "/data/refmac8-coot-0Wiso.pdb" XYZOUT "/tmp/lcocri/21_2_pdb_1.tmp" HKLIN > "/data/4_unique1.mtz" HKLOUT "/tmp/lcocri/21_3_mtz_1.tmp" LIBIN > "/data/ligand.cif" LIBOUT "/data/21_lib.cif" > > has failed with error message > > child killed: SIGABRT > > > *************************************************************************** > > > > > > #CCP4I TERMINATION STATUS 0 child killed: SIGABRT > > #CCP4I TERMINATION TIME 06 sep 2010 15:28:12 > > #CCP4I MESSAGE Task failed > > > > > > > > > > > > -- ___________________________________________________________________ Interactions faibles entre protéines en solution Costenaro L. (2010) Editions Universitaires Européennes, ISBN 9786131506048 Livre disponible en francais sur amazon: http://www.amazon.com/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=ISBN+9786131506048&x=0&y=0 ___________________________________________________________________ Dr. Lionel Costenaro Institut de Biologia Molecular de Barcelona - CSIC and Institute for Research in Biomedicine Parc Cientific de Barcelona C/ Baldiri i Reixac 10-12 E-08028 Barcelona, Spain Phone +34 93 403 49 57 Fax +34 93 403 49 79 Email [email protected] , [email protected] URL www.ibmb.csic.es , www.irbbarcelona.org
