[ccp4bb] Refmac bref MIXED failed
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 equal0.00 Not converging with gamma equal0.00 Trying gamma equal 5.503E-02 Not converging with gamma equal 5.503E-02 Trying gamma equal 0.1155000 . Not converging with gamma equal2655.967 Trying gamma equal2921.619 Not converging with gamma equal2921.619 Trying gamma equal3213.836 Gamma decreased to3155.393 *** * 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
Re: [ccp4bb] Refmac bref MIXED failed
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 equal0.00 Not converging with gamma equal0.00 Trying gamma equal 5.503E-02 Not converging with gamma equal 5.503E-02 Trying gamma equal 0.1155000 . Not converging with gamma equal2655.967 Trying gamma equal2921.619 Not converging with gamma equal2921.619 Trying gamma equal3213.836 Gamma decreased to3155.393 *** * 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
Re: [ccp4bb] Refmac bref MIXED failed
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 0.00 Not converging with gamma equal 0.00 Trying gamma equal 5.503E-02 Not converging with gamma equal 5.503E-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
Re: [ccp4bb] Refmac bref MIXED failed
Hi Garib, I tried with refmac 5.6 and the same inputs; it worked fine. Thanks, Lionel 2010/9/6 Garib N Murshudov ga...@ysbl.york.ac.uk 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 equal0.00 Not converging with gamma equal0.00 Trying gamma equal 5.503E-02 Not converging with gamma equal 5.503E-02 Trying gamma equal 0.1155000 . Not converging with gamma equal2655.967 Trying gamma equal2921.619 Not converging with gamma equal2921.619 Trying gamma equal3213.836 Gamma decreased to3155.393 *** * 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%3Dapsfield-keywords=ISBN+9786131506048x=0y=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 Emaillionel.costen...@ibmb.csic.es , lionel.costen...@irbbarcelona.org URL www.ibmb.csic.es , www.irbbarcelona.org
