Hi, I'm not sure whether it's related to the error you're seeing but as far as I know, in order for refmac to do mixed B-refinement (that is Biso and Baniso) you have to set yourself by editing (!!) the incoming pdb such that whichever atoms you'd like to have Biso refined should have only Biso in the input file. I suggested a while ago that this be fixed to become more elegant (say by specifying range of residues in the gui) but apparently it still works only the old way.
Cheers, Boaz ----- Original Message ----- From: Lionel Costenaro <lco...@ibmb.csic.es> Date: Monday, September 6, 2010 17:09 Subject: [ccp4bb] Refmac bref MIXED failed To: CCP4BB@JISCMAIL.AC.UK > 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 > Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan
