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Cannot Open Environ.def

for csh/tcsh setenv MALLOC_CHECK_ 0 or for sh MALLOC_CHECK_=0 export MALLOC_CHECK_ or for ksh/bash export MALLOC_CHECK_=0 Apple Mac OS X MS Windows Problems with building the I was wondering if anyone might have any ideas? Tim On Thu, Nov 11, 2010 at 12:57:44PM -0800, Jerry McCully wrote: > > Dear ALL; > > Recently we updated our CCP4 to 6.1.13 with CCP4Interface2.0.6. They are associated with file names of a form appropriate for the operating system, but including a name part and possibly an extension/type, directory specification and version. http://dekovsoft.com/cannot-open/cannot-open-an-anonymous-level-security-token-window-open.html

If it runs successfully a message like "Normal termination" will be printed with the timing information. Those in $CEXAM/unix/runnable can actually be run using the distributed data in $CEXAM/toxd, $CEXAM/rnase and $CEXAM/data. [edit] Output The 'log file' output may contain error messages and warnings. This page has been accessed 7,261 times. Contents 1 Command line arguments/file connection 2 Keyworded input 3 Examples 4 Output [edit] Command line arguments/file connection Input and output data files are specified by associating them with logical names.

You will also need the file symop.lib which should be in the logical directory $CLIBD, or MOSFLM will stop with an error later in its processing (specifically, when it wants to i.e. Aimin rotamer >>>>>> CCP4 library signal ccp4_general:Cannot open environ.def (Success) raised in ccp4fyp <<<<<< rotamer: Cannot open environ.def rotamer: Cannot open environ.def Times: User: 0.0s System: 0.0s Elapsed: 0:00 Previous message: Some log files are marked up in HTML, and can therefore be viewed in a browser such as Firefox.

Julien Vanwinsberghe RE: [ccp4bb]: Problem running CCP4: "Ca... where '<>' indicates place holders and '[ ]...' indicates optional repeated items i.e. It's not a permissions thing (I changed to 777, still got the error). Some will default to reading a library file (e.g.

CCP4 progs will not run correctly."setenv BINSORT_SCR $CCP4_SCR---------------------------------------------------------------... Unfortunately I don't seem to be able to get the example job (System Administration -> Configure Interface -> Test -> Running Task) to run. more info regarding computer in question (linux centos 64 bit) and such: echo $PATH /home/sylvie/buster/MakeTNT/bin:/home/sylvie/buster/scripts:/home/sylvie/buster/autoBUSTER/bin/linux64:/home/sylvie/buster/adm/bin:/usr/local/phenix-1.8-1069/build/intel-linux-2.6-x86_64/bin:/usr/local/xtal/XDS-INTEL64_Linux_x86_64:/usr/local/xtal/arp_warp_7.3/bin/bin-x86_64-Linux:/usr/local/xtal/ccp4-6.3.0/share/dbccp4i/bin:/usr/local/xtal/ccp4-6.3.0/share/ccp4i/bin:/usr/local/xtal/ccp4-6.3.0/bin:/usr/local/xtal/ccp4-6.3.0/etc:/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/usr/local/xtal/ccp4-6.3.0/share/xia2/xia2core//Test:/usr/local/xtal/ccp4-6.3.0/share/xia2/xia2//Applications:/home/sylvie/bin -- ***************************************** Rosa Grenha, PhD I.B.B.M.C. I'm currently only running on "localhost" (I'll move it to PBS/Torque once I get it running).

Some common logical names with default extensions are: HKLIN: input MTZ reflection file (.mtz) HKLOUT: output MTZ reflection file (.mtz) MAPIN: input map file (.map) MAPOUT: output map file (.map) XYZIN: If you've done this already then that's more of a mystery! This can be fixed by editing the "setup" file in the top-level of the build-it-yourself distribution of Mosflm, and change the line that sets the environment variable "X11_LIBS" to reflect where or # is treated as a comment and ignored.

The condition code set by the program will indicate success or failure as appropriate for the operating system, e.g. Such arguments are separated by spaces, tabs, commas or = characters. of symmetry operators) or writing a file in the scratch directory, and usually are not specified. A continuation character may precede the comment; Strings may be single- or double-quoted but the quotes may be omitted if a string doesn't contain whitespace or a comment or continuation character

This is set in the modulefile as: CINCL=/software/modules/ccp4/6.1.2/ccp4-6.1.2/include I've tried symlinking the environ.def (found in /software/modules/ccp4/6.1.2/ccp4-6.1.2/shared) into the directory, but it didn't seem to fix things. navigate here and the .bashrc contains following entries:---------------------------------------------------------------PATH="$PATH:/usr/local/software/ccp4/ccp4-6.0.2/bin/"PATH="$PATH:/usr/local/software/ccp4/ccp4-6.0.2/include/"/usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup-bash---------------------------------------------------------------All the files have the according permissions. If you want to add environment (like sourcing CCP4/include/ccp4.setup-sh) you need to add it to setenv.sh in this directory. and in case you were wondering about the location of my programs: CCP4 /usr/local/xtal/ccp4-6.3.0 and buster /home/sylvie/buster ***** *this is the error shown on the top of the mtzchk log:* >>>>>>

Flip Hoedemaeker Reply via email to Search the site The Mail Archive home ccp4bb - all messages ccp4bb - about the list Expand Previous message Next message The Mail Archive home zero or more. EikeCCP4bb navigationCCP4bb <-- 2008 <-- May 2008 <-- 16 May 2008Previous message:Subject: Re: Phaser compile errorsFrom: Nathan I Nicely nathan {- dot -} nicely {- at -} DUKE {- dot -} http://dekovsoft.com/cannot-open/unable-to-open-connection-to-com3-unable-to-open-serial-port.html Problems when running the program All platforms No such file or directory Linux errors *** glibc detected *** mosflm: double free or corruption (!prev): Mac OSX errors MS-Windows errors Problems with

Rosa Grenha Re: [ccp4bb] Problem running Buster (mtzdump: Cannot... Graphs appear as Java applets. I read somewhere that ccp4fyp looks at the $CINCL variable.

several input reflection files.

[sharp-discuss] mtz check fails during buster run Eugene Valkov eugene.valkov at gmail.com Tue Aug 16 13:04:31 CEST 2011 Previous message: [sharp-discuss] mtz check fails during buster run Next message: [sharp-discuss] Error You'd be doing this at your own risk > and don't recommend this! > > The information in mtzchk.2.log: > > >>>>>> CCP4 library signal ccp4_general:Cannot open environ.def (Error) > raised A concrete example is fft hklin native-Fs.mtz mapout 2Fo-Fc.map Here an fft is performed on the MTZ reflection dataset associated with the logical name hklin (filename native-Fs.mtz) and a map is It's complaining it can't open environ.def.

Many thanks Eugene 2011/8/16 Miguel Ortiz Lombardía : > On 16/08/11 12:39, Eugene Valkov wrote: >> Dear all, >> >> I'm unable to run Buster as it keeps reporting Linux errors Failure to link You may get an error like: /usr/bin/gfortran -m32 -s -static -static-libgcc control.o mosflm_all_ip_inc.o unoptimizable.o pck.o ctimer.o chelp.o open_socket.o close_socket.o read_socket.o write_socket.o mosflm_jpeg.o matzerr.o hklmanage.o torefix.o bravais_fortran.o Did someone else have the same experience ? this contact form The rules for matching logical names with the default specifications given above then apply to the prefix of the name which matches the entries in the files $CINCL/environ.def and $CINCL/default.def.

If you don't want to do these checks (and want to use the MTZ file as it is): please use the command-line option UseMtzchk="no". Otherwise, if a file isn't given for the logical name, the program will attempt to open a file in the current directory with a name corresponding to the logical name. These usually get set up by sourcing the $CCP4/include/ccp4-setup.X file appropriate for your shell. I have installed ccp4-6.3.0 and buster gives me now an error related to environ.def It runs without any problems with the previous version of ccp4 and the exact same files, in

However, there is an error when we ran autobuster. > > The error messenge from Buster: > > a check of the input MTZ file > (test.mtz) gave an > error The association is usually made by specifying name/value pairs on the command line following the program name. Claus Flensburg Re: [ccp4bb] Problem running Buster (mtzdump: Ca... In this case they are typically specified as HKLINn, for instance, where n is a sequence number.

If you don't want to > do these checks (and want to use the MTZ file as it > is): please use the command-line option > UseMtzchk="no". You can see from the above that the Mosflm build is expecting to find the X11 libraries in "/usr/X11R6/lib"; that's where they would have been traditionally, but newer distributions of Linux However, there are some general rules: Only the first four characters of keywords are significant (although you are recommended to use complete keywords) and they are case-insensitive; Records may be continued in Unix, zero for success, non-zero on error.

This is caused by an error in the cbf reading routines. This is plain old shell, not (t)csh. Bât 430 University Paris XI 91 405 ORSAY Cedex 1 France Tel: +33 1 69157970 Fax: +33 1 69853715 Email: [email protected] Previous message View by thread View by date Next message Rosa Grenha Reply via email to Search the site The Mail Archive home ccp4bb - all messages ccp4bb - about the list Expand Previous message Next message The Mail Archive home

I previously corrected it adding "C:\Program Files\CCP4-Packages\ccp4-6.0\include" to the windows PATH, but I see this error again when I try to call CCP4 from TomCat, in a JSP web page. Try it now. > http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > Previous message View by thread View by date Next message [ccp4bb] Problem again with mosflm michael nelson Re: [ccp4bb] Problem again with mosflm William Scott I would greatly appreciate any help on solving this problem.Thanks a lot in advance and have a nice weekend. The job's log looks like this: #CCP4I VERSION CCP4Interface 2.0.5 #CCP4I SCRIPT LOG import #CCP4I DATE 09 Dec 2009 16:16:44 #CCP4I USER markbate #CCP4I PROJECT PROJECT #CCP4I JOB_ID 4 #CCP4I SCRATCH

I had a bit of trouble getting the source code to build in our environment, so I grabbed the contents of the Mac OS X package & changed some of the changing the line: CCP4="/xtal/CCP4/ccp4-6.1.13" in $BDG_home/machines/*/ccp4.setup to: CCP4="/xtal/CCP4/ccp4-6.2.0" did the trick! Names from this set which are appropriate to each program are detailed in the programs write-ups.