[ccp4bb] problem starting refmac from ccp4i gui
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
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
[ccp4bb] error in ccp4i
hi there, I'm using ccp4 installed via fink on my macbook pro, and suddenly the program complains that it cannot connect to the database server and won't let me run a combat job with the following error: Using CCP4 programs from /sw/share/xtal/ccp4-6.1.1/bin CCP4i failed to connect to database server after 1 attempt(s) Accessing the project database directly for this session ERROR opening socket connection in NotifyDatabase: Arguments: 159 hect UpdateStatus RUNNING -pid 916 SERVER_HOST: localhost SERVER_PORT: 4441 Error : couldn't open socket: host is unreachable ERROR opening socket connection in NotifyDatabase: Arguments: 159 hect UpdateStatus FINISHED SERVER_HOST: localhost SERVER_PORT: 4441 Error : couldn't open socket: host is unreachable Any clue? thanks a lot, ciao s PS: I'm right now at the ESRF, is there a kind of synchrotron-related issue (when you desperately need a software, that's when it goes down!) -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094
