Hi Boaz,
Thanks for your suggestion. I have tried as you suggested. In my case,
CCP4_MASTER
can NOT set to be /home/prog.
The ccp4i did not launched because it can not locate the ccp4i.tcl file.
On Tue, Sep 30, 2008 at 8:53 PM, Boaz Shaanan <[EMAIL PROTECTED]> wrote:
> Your setup in ccp4.setup seems to be incorrect.
> You should have:
> setenv CCP4_MASTER /home/prog
>
> and then you would have:
>
> echo $CCP4 /home/prog/ccp4-6.0.2
>
> I don´t think your problem has anything to do with tcl setup.
>
> Boaz
>
> ----- Original Message -----
> From: Yingjie Peng <[EMAIL PROTECTED]>
> Date: Tuesday, September 30, 2008 15:45
> Subject: Re: [ccp4bb] CCP4i can NOT run
> To: CCP4BB@JISCMAIL.AC.UK
>
> > 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-
> > machinesite.
> >
> > 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/helpsetenv 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
> > >>
> > >>
> > >>
> > >
> >
>
> 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
>
