Hi Iain, Thanks for your reply. The path for tclsh is "/usr/local/tcltkblt/bin/". There are six files: bltsh, bltwish, tclsh, tclsh8.4, wish and wish8.4. The tclsh and wish are symbolic links for tclsh8.4 and wish8.4, respectively. For the permission reason you mentioned, I have also tried this change: sudo chown yjpeng:yjpeng -R /usr/local/tcltkblt It does NOT work!
For better analysis, I paste my ccp4.setup file as following: ################### THIS SECTION MUST BE EDITED ##################### # CCP4_MASTER is the location of the top-level directory containing `ccp4-<version>' # This is usually the directory in which you ran the tar command to unpack the # code, and is assumed to be shared between machines at a multi-machine site. setenv CCP4_MASTER /home/prog/ccp4-6.0.2 setenv CCP4 $CCP4_MASTER/ccp4-6.0.2 # Check for existence of CCP4_MASTER if (! -e $CCP4_MASTER) then echo "********************* WARNING **********************" echo "The directory $CCP4_MASTER" echo "(assigned to CCP4_MASTER) does not exist." echo "The CCP4 programs will not run correctly, and any" echo "installation attempt will have errors or will fail." echo "********************* WARNING **********************" endif # CCP4_SCR: a per-user directory for run-time-generated scratch # files. A dedicated scratch filesystem is probably better than (/usr)/tmp # BINSORT_SCR: a scratch directory for binsort's use; normally same as CCP4_SCR setenv CCP4_SCR /data/tmp # check to see if this exists and if not try to make it if (! -e $CCP4_SCR) mkdir $CCP4_SCR if (! -e $CCP4_SCR) \ echo "Unable to make CCP4_SCR. CCP4 progs will not run correctly." setenv BINSORT_SCR $CCP4_SCR ### CCP4i setup - you may need to edit CCP4I_TCLTK ### # CCP4I_TOP - the top directory of the interface setenv CCP4I_TOP ${CCP4}/ccp4i # CCP4I_TCLTK - directory containing tclsh,wish and bltwish executables # as used in $CCP4I_TOP/bin/ccp4i,ccp4ish,loggraph # For 'standard' installations this is /usr/local/bin # but note the SGI distributed version of Tcl/Tk is not # appropriate version setenv CCP4I_TCLTK /usr/local/tcltkblt/bin # CCP4I_HELP - directory contain ccp4i help - default is $CCP4I_TOP/help setenv CCP4I_HELP ${CCP4I_TOP}/help ### Optional - setting http_proxy environment # The commented out 'setenv' line below may have to be declared to download # and edit protein sequences using the new "Import/Edit Protein Sequences" # (This may also be required for remote job submission in arp/warp.) # task. If so, uncomment this line and replace the example proxy URL with your # relevant URL #setenv HTTP_PROXY wwwblah.blah.ac.uk:xxxx/blah.blah ################### NOVICE USERS STOP HERE ##################### ################### OPTIONS TO CUSTOMISE CCP4 ##################### # By default, CCP4 directories are appended to the end of paths (PATH, # LD_LIBRARY_PATH, and DYLD_LIBRARY_PATH). If ccp4_first_in_path is set # to 1, then they will be prepended to the beginning of paths. # When deciding local policy, bear in mind the possible existence of # other CCP4 installations, and the possibility of non-CCP4 programs # with conflicting names. set ccp4_first_in_path = 1 # The commented-out switch statement below provides an example of how # to use this file for several machines/architectures sharing $CCP4_MASTER. # If necessary, uncomment and edit this. Otherwise, if you're only supporting # a single system alter the uncommented part as necessary. # # The significance of the environment variables is as follows: # CBIN: location of the executables -- must be on your path (see below); # CLIB: location of (binary) library files such as libccp4.a and libccp4.so; # MANPATH: set this if your system's `man' looks at such an environment # variable to determine where to look for man pages. By adding # $CCP4/man to the normal path you get the CCP4 man pages # with keyword searching as system ones. # MCTYPE: used for LAUE make -- see LAUE documentation # CCP4_BROWSER: set this if you intend to use the html documentation # (recommended). It should have the path and name of a html browser eg # /usr/bin/X11/netscape or /usr/local/bin/lynx. The browser will be # started with the alias ccp4help and will open the file # $CHTML/INDEX.html. # switch (`hostname`) # edit this switch statement if used # # for multiple systems # case 'foo': setenv CBIN $CCP4/bin setenv CLIB $CCP4/lib setenv CCP4_BROWSER firefox if (${?MANPATH}) then if ($ccp4_first_in_path) then setenv MANPATH ${CCP4}/man:${MANPATH} else setenv MANPATH ${MANPATH}:${CCP4}/man endif else if ($ccp4_first_in_path) then setenv MANPATH ${CCP4}/man:/usr/share/man else setenv MANPATH /usr/share/man:${CCP4}/man endif endif setenv MCTYPE unix # (only for Laue) # breaksw # default: # echo "CCP4 not implemented on this system" # exit 1 # breaksw # endsw switch (`uname`) case 'Darwin': limit stacksize 65536 breaksw default: breaksw endsw # The following are for all systems setenv CCP4_LIB $CLIB setenv CCP4_BIN $CBIN # CLASSPATH for Java if (${?CLASSPATH}) then if ($ccp4_first_in_path) then setenv CLASSPATH ${CBIN}:${CLASSPATH} else setenv CLASSPATH ${CLASSPATH}:${CBIN} endif else if ($ccp4_first_in_path) then setenv CLASSPATH ${CBIN}:. else setenv CLASSPATH .:${CBIN} endif endif ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ### setenv PLOT_COMMAND 'lp -s -dmicrolaser' setenv PRINT_COMMAND 'lp -s -denscript' # HARVESTHOME specifies location of harvesting files (defaults to $HOME) #setenv HARVESTHOME ### CCP4_OPEN ### # CCP4_OPEN may be set to 'UNKNOWN' to stop open failures for files opened # as NEW that already exist. Novices should use 'NEW' to avoid inadvertant # over-writing of existing files, which is then treated as a fatal error. setenv CCP4_OPEN UNKNOWN ### BINSORT_MEM ### # BINSORT_MEM is workspace used by the binsort program. In principle this # value is machine-dependent. It may benefit from being enlarged, but values # higher than 2M have been reported to cause excessive paging on some systems. # You might like to experiment with a program such as fft with different # values -- 102400 (bytes) is the default. csh's `time' command can tell you # about paging. # # setenv BINSORT_MEM 8388608 # LD_LIBRARY_PATH specifies where to find dynamic libraries (e.g. libccp4.so) # at runtime if (${?LD_LIBRARY_PATH}) then if ($ccp4_first_in_path) then setenv LD_LIBRARY_PATH ${CLIB}:${LD_LIBRARY_PATH}:${CCP4}/extralib else setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${CLIB}:${CCP4}/extralib endif else setenv LD_LIBRARY_PATH ${CLIB}:${CCP4}/extralib endif # DYLD_LIBRARY_PATH specifies where to find dynamic libraries (e.g. libccp4.dylib) # at runtime (used on Mac OS X) if (${?DYLD_LIBRARY_PATH}) then if ($ccp4_first_in_path) then setenv DYLD_LIBRARY_PATH ${CLIB}:${CCP4}/extralib:${DYLD_LIBRARY_PATH} else setenv DYLD_LIBRARY_PATH ${DYLD_LIBRARY_PATH}:${CLIB}:${CCP4}/extralib endif else setenv DYLD_LIBRARY_PATH ${CLIB}:${CCP4}/extralib endif ### XAPPLRESDIR ### # If you want to use xloggraph/xplot84driver, you need to get the application # defaults picked up somehow. As distributed, the file can't just live in an # application defaults directory since it requires reading by xrdb to sort out # the differences for monochrome displays. At Daresbury a version of the file # assuming a monochrome display is kept in the directory # $CCP4_LIB/X11/app-defaults and this is picked up through the # XUSERFILESEARCHPATH environment variable. That means you only see black and # white on a colour display. Alternatively you might make sure that it is # read by xrdb on startup of the X Windows system or delegate the # responsibility to users to run it. There are disadvantages to putting an # invocation of xrdb in here, one being that the correct value of DISPLAY may # not be set at the time this file is read. Thus edit this part as # appropriate. (SunOS will normally want to use /usr/openwin or $OPENWINHOME # instead of /usr; others may want /usr/local/lib or somw such): if ($?XUSERFILESEARCHPATH) then setenv XUSERFILESEARCHPATH $CCP4_LIB/X11/app-defaults/%N:$XUSERFILESEARCHPATH else setenv XUSERFILESEARCHPATH $CCP4_LIB/X11/app-defaults/%N:/usr/lib/X11/app-defaults endif ### TRAPPFE ### # TRAPFPE is set to ensure (in collaboration with -lfpe) an abort on floating # point exceptions under IRIX. It shouldn't cause harm on other systems, but # edit this to comment it out if necessary. setenv TRAP_FPE "OVERFL=ABORT; DIVZERO=ABORT; INVALID=ABORT" # The following can be used to put a message of the day to announce news about # CCP4 or whatever to CCP4 users. You might also want to edit this part to # have machine-specific messages dependent on `hostname`. if (-e $CCP4/include/ccp4.msg) cat $CCP4/include/ccp4.msg ################### EXPERIENCED USERS STOP HERE ##################### Thanks very much. Best regards, Yingjie On Tue, Sep 30, 2008 at 10:59 AM, Iain Kerr <[EMAIL PROTECTED]> wrote: > Hello Yingjie > > Tclsh handles the starting and running of jobs, so it must be a problem > with this. If you are able to startup the GUI then your path is correct is > ccp4.setup..where are the bltwish (wish) and tclsh /usr/local/bin ? > > If the tclsh executable is called something like "tclsh8.4" then CCP4i will > not recognise it..you have to make a symbolic link to the executable, in the > same directory, as below: > > ln -s tclsh8.4 tclsh (or the other way round, check)..also make sure you > have read (and possibly execute) permission for this directory and the files > within. > > HTH, > Iain > > Yingjie Peng wrote: > >> Dear friends, >> I have installed the latest version of CCP4i under Fedora 9 on my laptop >> HP Compaq 6515b (two processors). The system >> setup was done and the CCP4i interface can run normally. But if I submit a >> job, it displayes "STARTING" the job in the job window >> and will NOT actually run the job. Also I can NOT kill the job with its >> status as STARTING. >> I have checked my Tcl/tk is version 8.4 and the CCP4I_TCLTK environment >> variable is pointed to the right directory containing >> tclsh, bltwish and other files. >> Is there any suggestion on how to solve this problem? Thank you very much >> in advance. >> Best wishes, >> Yingjie >> Yingjie PENG, Ph.D. student >> Structural Biology Group >> Shanghai Institute of Biochemistry and Cell Biology (SIBCB) >> Shanghai Institute of Biological Sciences (SIBS) >> Chinese Academy of Sciences (CAS) >> 320 Yue Yang Road, Shanghai 200031 >> P. R. China >> 86-21-54921117 >> Email: [EMAIL PROTECTED] >> ------------------------------------------------------------------------ >> >> >> No virus found in this incoming message. >> Checked by AVG - http://www.avg.com Version: 8.0.173 / Virus Database: >> 270.7.5/1698 - Release Date: 9/29/2008 7:25 PM >> >> >> >