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 I would greatly appreciate any help on solving this problem.Thanks a lot in advance and have a nice weekend. Many of the programs produce graphical information. Graphs appear as Java applets. http://culturahq.com/cannot-open/cannot-open-an-anonymous-level-security-token-window-open.html
Eventhough my ccp4 installation seemed to work fine all the way MTZDUMPand the applications which use it (namely refmac ...) unfortunatly failwith the following error: --------------------------------------------------------------->>>>>> CCP4 library signal ccp4_general:Cannot open 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 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. Thanks Julien Vanwinsberghe Previous message View by thread View by date Next message RE: [ccp4bb]: Problem running CCP4: "Cannot open... http://www.globalphasing.com/pipermail/sharp-discuss/2011-August/002054.html
In this case they are typically specified as HKLINn, for instance, where n is a sequence number. Many thanks Eugene 2011/8/16 Miguel Ortiz Lombardía
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. 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. Mobile. We recommend installing the CCP4 suite, since MOSFLM writes its reflection data to an MTZ file, a binary file which is most easily read by CCP4 programs. Linux When reading
Thus the format of a program invocation is
Postdoctoral Research Fellow Sanger Building Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK email: ev269 at cam.ac.uk tel: +44 (0)1223 760 468 fax: +44 (0)1223 Over-writing will occur if the value of the variable is UNKNOWN; otherwise the program will abort.  Keyworded input Most programs take 'keyworded' input to set their parameters. 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. Unfortunately I don't seem to be able to get the example job (System Administration -> Configure Interface -> Test -> Running Task) to run.
I read somewhere that ccp4fyp looks at the $CINCL variable. https:[email protected]/msg13525.html zero or more. 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 I'm currently only running on "localhost" (I'll move it to PBS/Torque once I get it running).
Some will default to reading a library file (e.g. have a peek at these guys michael nelson wrote: > Sorry folks, but I have been very frustrated to get > mosflm and imosflm to work. > I have get around with X11, but I got another 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". Julien Vanwinsberghe RE: [ccp4bb]: Problem running CCP4: "Ca...
Thank you nevertheless Julien V. The cure is currently to set the environment variable MALLOC_CHECK_ (note the trailing underscore character) to zero. 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 check over here 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
If this file doesn't exist, add it and all should be well. Names from this set which are appropriate to each program are detailed in the programs write-ups. 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:* >>>>>>
Winter, G \(Graeme\) Re: [ccp4bb]: Problem running CCP4: "Cannot... A dedicated scratch filesystem is probably better than(/usr)/tmp# BINSORT_SCR: a scratch directory for binsort's use; normally same asCCP4_SCRsetenv CCP4_SCR /tmp/$USER # check to see if this exists and if not try If you've done this already then that's more of a mystery! http://culturahq.com/cannot-open/cannot-open-cd-udf-2-0.html Some log files are marked up in HTML, and can therefore be viewed in a browser such as Firefox.
where '<>' indicates place holders and '[ ]...' indicates optional repeated items i.e. Retrieved from "http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=How_to_run_CCP4_programs_from_the_command_line" Views Article Discussion Edit History Personal tools Log in / create account Navigation Main Page Community portal Current events Recent changes Random page Help Donations Search Toolbox I found a modulefile on the bulletin board (http:[email protected]/msg10981.html), which I changed a little to suit our setup. and the .bashrc contains following entries:---------------------------------------------------------------PATH="$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.
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 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 Did someone else have the same experience ? 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
If it runs successfully a message like "Normal termination" will be printed with the timing information. 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. All the CCP4 programs work fine as far as I can >> tell, and I can use the data in REFMAC without any issues. >> >> Any advice will be much 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.
The detail of the input expected is given in the documentation for each program, of course. After a few tweaks to the module file, I managed to get ccp4i going on the cluster. or # is treated as a comment and ignored. Although problems running the program may be due to errors in the build, they are not dealt with in this section.
For details > see above and ./mtzchk.2.log. There is a library of standard logical names with associated default extensions and access modes (read, write or read/write). Those in $CEXAM/unix/runnable can actually be run using the distributed data in $CEXAM/toxd, $CEXAM/rnase and $CEXAM/data.  Output The 'log file' output may contain error messages and warnings. This is caused by an error in the cbf reading routines.
parameters and option specifications are read on the standard input stream and a 'log file' of printed output is produced on the standard output stream. The condition code set by the program will indicate success or failure as appropriate for the operating system, e.g.