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Cannot Open Environ.def

If you want to add environment (like sourcing CCP4/include/ccp4.setup-sh) you need to add it to setenv.sh in this directory. This page has been accessed 7,261 times. 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: 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. have a peek at this web-site

It's not a permissions thing (I changed to 777, still got the error). Graphs appear as Java applets. Although problems running the program may be due to errors in the build, they are not dealt with in this section. Retrieved from "http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=How_to_run_CCP4_programs_from_the_command_line" Views Article Discussion Edit History Personal tools Log in / create account Navigation Main Page Community portal Current events Recent changes Random page Help Donations Search Toolbox

I would greatly appreciate any help on solving this problem.Thanks a lot in advance and have a nice weekend. 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. 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

The condition code set by the program will indicate success or failure as appropriate for the operating system, e.g. EikeCCP4bb navigationCCP4bb <-- 2008 <-- May 2008 <-- 16 May 2008Previous message:Subject: Re: Phaser compile errorsFrom: Nathan I Nicely nathan {- dot -} nicely {- at -} DUKE {- dot -} 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 It's complaining it can't open environ.def.

I was wondering if anyone might have any ideas? There is a library of standard logical names with associated default extensions and access modes (read, write or read/write). This is read on the standard input in the form of records with a leading keyword followed, possibly, by arguments which might be numbers or strings or keyword/value pairs of the https://www.mail-archive.com/[email protected]/msg02284.html CCP4 progs will not run correctly."setenv BINSORT_SCR $CCP4_SCR---------------------------------------------------------------...

These usually get set up by sourcing the $CCP4/include/ccp4-setup.X file appropriate for your shell. 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 This input is usually keyworded. Logical names are alphanumeric, possibly also including underscores.

In this case they are typically specified as HKLINn, for instance, where n is a sequence number. 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. I read somewhere that ccp4fyp looks at the $CINCL variable. If you've done this already then that's more of a mystery!

If this file doesn't exist, add it and all should be well. http://sauvblog.com/cannot-open/cannot-open-ws2-32-lib.html This is caused by an error in the cbf reading routines. 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". Many of the programs produce graphical information.

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 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 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. Source Mark Bate Wed, 09 Dec 2009 15:34:18 -0800 Hi, I'm trying to get CCP4 (6.1.2) suite up and running on our shiny new Xserve cluster.

Over-writing will occur if the value of the variable is UNKNOWN; otherwise the program will abort. [edit] Keyworded input Most programs take 'keyworded' input to set their parameters. 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. or # is treated as a comment and ignored.


zero or more. 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. Thank you nevertheless Julien V. 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 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 If it runs successfully a message like "Normal termination" will be printed with the timing information. have a peek here For details see above and busterTest10/mtzchk.2.log.

Did someone else have the same experience ?