Re: [ccp4bb] problem starting refmac from ccp4i gui
Boaz, I recently saw the same message, after installing (binary) 6.1.1 . The workaround that seems to work for me is to start a new project from scratch. The STARTING problem may have to do with the line 127.0.0.1 localhost.localdomain localhost missing from /etc/hosts - did you check that? HTH, Kay Boaz Shaanan schrieb: Hi, On a newly installed v 6.1.1 I (built from source) I can't get refmac to start from the gui (other programs, such as pointless and phaser, run fine). The latest patches have also been installed. When I start a refmac job that runs file under 6.1.0 (the binary built) the job gets stuck and the gui reports 'starting' for the job without switching to 'running'. The latest refmac version from York is installed (5.0.92) and again, it runs fine under 6.1.0. These lines appear in the window from which the ccp4i was launched after starting the job: can't set ATOM(0): variable isn't array while executing set [subst $root]([subst $indx0]) (procedure ExecuteScript line 50) invoked from within ExecuteScript $system(SCRIPT) (script arm line 8) invoked from within switch $system(RUN_MODE) \ script { source [file join $env(CCP4I_TOP) src execute.tcl] source [file join $env(CCP4I_TOP) src job_utils... (file /home/boaz/ccp4/ccp4-6.1.1/ccp4i/bin/ccp4ish.tcl line 145) invoked from within source [file join $env(CCP4I_TOP) bin ccp4ish.tcl] (file /home/boaz/ccp4/ccp4-6.1.1/ccp4i/bin/ccp4ish line 12) Does anybody have a clue on what could have gone wrong and how to fix the problem ? Thanks, Boaz 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 smime.p7s Description: S/MIME Cryptographic Signature
Re: [ccp4bb] problem starting refmac from ccp4i gui
Hi, If you were trying to re-run a job created with ccp4 6.1.0 or earlier, this is a known bug. Have a look at: http://www.ccp4.ac.uk/problems.php#6.1.1-programs If that is the case, there is a new refmac.tcl file that solves that problem. Best, Miguel Le 16 mai 09 à 12:42, Kay Diederichs a écrit : Boaz, I recently saw the same message, after installing (binary) 6.1.1 . The workaround that seems to work for me is to start a new project from scratch. The STARTING problem may have to do with the line 127.0.0.1 localhost.localdomain localhost missing from /etc/hosts - did you check that? HTH, Kay Boaz Shaanan schrieb: Hi, On a newly installed v 6.1.1 I (built from source) I can't get refmac to start from the gui (other programs, such as pointless and phaser, run fine). The latest patches have also been installed. When I start a refmac job that runs file under 6.1.0 (the binary built) the job gets stuck and the gui reports 'starting' for the job without switching to 'running'. The latest refmac version from York is installed (5.0.92) and again, it runs fine under 6.1.0. These lines appear in the window from which the ccp4i was launched after starting the job: can't set ATOM(0): variable isn't array while executing set [subst $root]([subst $indx0]) (procedure ExecuteScript line 50) invoked from within ExecuteScript $system(SCRIPT) (script arm line 8) invoked from within switch $system(RUN_MODE) \ script { source [file join $env(CCP4I_TOP) src execute.tcl] source [file join $env(CCP4I_TOP) src job_utils... (file /home/boaz/ccp4/ccp4-6.1.1/ccp4i/bin/ccp4ish.tcl line 145) invoked from within source [file join $env(CCP4I_TOP) bin ccp4ish.tcl] (file /home/boaz/ccp4/ccp4-6.1.1/ccp4i/bin/ccp4ish line 12) Does anybody have a clue on what could have gone wrong and how to fix the problem ? Thanks, Boaz 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 -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée ) Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] problem starting refmac from ccp4i gui
Hi Kay, As usual, your remedy works. I started in a new project (subdirectory of the former one) and all is OK. The job runs fine and there is no frozen 'starting' declaration anymore. I'm still puzzled why it happens with refmac and not with e.g. phaser, scala, pointless (all are programs that I ran in this project with 6.1.0 and earlier versions). I hope the ccp4 guys fix the problem soon. Thanks for your help. Cheers, Boaz - Original Message - From: Kay Diederichs kay.diederi...@uni-konstanz.de Date: Saturday, May 16, 2009 13:43 Subject: Re: [ccp4bb] problem starting refmac from ccp4i gui To: CCP4BB@JISCMAIL.AC.UK Boaz, I recently saw the same message, after installing (binary) 6.1.1 . The workaround that seems to work for me is to start a new project from scratch. The STARTING problem may have to do with the line 127.0.0.1 localhost.localdomain localhost missing from /etc/hosts - did you check that? HTH, Kay Boaz Shaanan schrieb: Hi, On a newly installed v 6.1.1 I (built from source) I can't get refmac to start from the gui (other programs, such as pointless and phaser, run fine). The latest patches have also been installed. When I start a refmac job that runs file under 6.1.0 (the binary built) the job gets stuck and the gui reports 'starting' for the job without switching to 'running'. The latest refmac version from York is installed (5.0.92) and again, it runs fine under 6.1.0. These lines appear in the window from which the ccp4i was launched after starting the job: can't set ATOM(0): variable isn't array while executing set [subst $root]([subst $indx0]) (procedure ExecuteScript line 50) invoked from within ExecuteScript $system(SCRIPT) (script arm line 8) invoked from within switch $system(RUN_MODE) \ script { source [file join $env(CCP4I_TOP) src execute.tcl] source [file join $env(CCP4I_TOP) src job_utils... (file /home/boaz/ccp4/ccp4- 6.1.1/ccp4i/bin/ccp4ish.tcl line 145) invoked from within source [file join $env(CCP4I_TOP) bin ccp4ish.tcl] (file /home/boaz/ccp4/ccp4- 6.1.1/ccp4i/bin/ccp4ish line 12) Does anybody have a clue on what could have gone wrong and how to fix the problem ? Thanks, Boaz 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 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] problem starting refmac from ccp4i gui
Hi, This solved the problem too, thanks. I assumed the fixes you pointed out were included in the patch files in the ccp4 download area. Boaz - Original Message - From: Miguel Ortiz Lombardia miguel.ortiz-lombar...@afmb.univ-mrs.fr Date: Saturday, May 16, 2009 15:09 Subject: Re: [ccp4bb] problem starting refmac from ccp4i gui To: CCP4BB@JISCMAIL.AC.UK Hi, If you were trying to re-run a job created with ccp4 6.1.0 or earlier, this is a known bug. Have a look at: http://www.ccp4.ac.uk/problems.php#6.1.1-programs If that is the case, there is a new refmac.tcl file that solves that problem. Best, Miguel Le 16 mai 09 à 12:42, Kay Diederichs a écrit : Boaz, I recently saw the same message, after installing (binary) 6.1.1 . The workaround that seems to work for me is to start a new project from scratch. The STARTING problem may have to do with the line 127.0.0.1 localhost.localdomain localhost missing from /etc/hosts - did you check that? HTH, Kay Boaz Shaanan schrieb: Hi, On a newly installed v 6.1.1 I (built from source) I can't get refmac to start from the gui (other programs, such as pointless and phaser, run fine). The latest patches have also been installed. When I start a refmac job that runs file under 6.1.0 (the binary built) the job gets stuck and the gui reports 'starting' for the job without switching to 'running'. The latest refmac version from York is installed (5.0.92) and again, it runs fine under 6.1.0. These lines appear in the window from which the ccp4i was launched after starting the job: can't set ATOM(0): variable isn't array while executing set [subst $root]([subst $indx0]) (procedure ExecuteScript line 50) invoked from within ExecuteScript $system(SCRIPT) (script arm line 8) invoked from within switch $system(RUN_MODE) \ script { source [file join $env(CCP4I_TOP) src execute.tcl] source [file join $env(CCP4I_TOP) src job_utils... (file /home/boaz/ccp4/ccp4- 6.1.1/ccp4i/bin/ccp4ish.tcl line 145) invoked from within source [file join $env(CCP4I_TOP) bin ccp4ish.tcl] (file /home/boaz/ccp4/ccp4- 6.1.1/ccp4i/bin/ccp4ish line 12) Does anybody have a clue on what could have gone wrong and how to fix the problem ? Thanks, Boaz 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 -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée ) Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. 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