Hi Ian,
Improving the CCP4 tests is a priority. We (the core team) have a project
looking into that. If developers have their own tests for components of the
suite that have not made it into the distribution, then we'd be happy to
collect them for the new test set.
Best wishes
-- David
On 29 April 2014 11:59, Ian Tickle <[log in to unmask]> wrote:
> Hi Felix
>
> You're very trusting! Bugs in new versions of software are not unknown!
> The bug may not manifest itself in a program crash (though it makes life
> easier if it does), rather it may simply give different numerical results
> that you may not spot for some after. This is why CCP4 distributes test
> data (in $CEXAM) for users to test the software (though the examples there
> are hardly comprehensive). Most major software packages (e.g. LAPACK)
> provide comprehensive test suites that test all possible ways in which the
> software may be used so you can verify that the new version at least gives
> the same results as the distributor's test suite (this also checks whether
> there are machine dependencies). So I need to run tests on the new version
> & compare with results from the old one before I release it to users, for
> which I obviously need access to both versions. Also the man pages are
> missing from the new version: I just find it quicker & easier to type 'man
> fft' or whatever than to fire up the browser.
>
> Cheers
>
> -- Ian
>
>
> On 29 April 2014 11:23, Felix Frolow <[log in to unmask]> wrote:
>
>> Hi Tim,
>> What can be a reason to work with an obsolete version of CCP4?
>> I remember reading somewhere that 6.3.0 version is obsolete.
>>
>> FF
>>
>> Dr Felix Frolow
>> Professor of Structural Biology and Biotechnology, Department of
>> Molecular Microbiology and Biotechnology
>> Tel Aviv University 69978, Israel
>>
>> Acta Crystallographica F, co-editor
>>
>> e-mail: [log in to unmask]
>> Tel: ++972-3640-8723
>> Fax: ++972-3640-9407
>> Cellular: 0547 459 608
>>
>> On Apr 28, 2014, at 19:01 , Tim Gruene <[log in to unmask]> wrote:
>>
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> Dear Sreetama, dear Ian,
>>
>> I avoid sourcing both version 6.3 and 6.4 in the same terminal. If I
>> need to work with 6.3 I modify my .bashrc from 6.4 to 6.3 and then
>> open a new terminal to make sure everything refers to v6.3 and vice versa.
>>
>> Best,
>> Tim
>>
>>
>> On 04/28/2014 04:51 PM, Ian Tickle wrote:
>>
>> Harry,
>>
>> I've run into this problem before with other programs when I switch
>> between v6.3 & v6.4. I think the problem is this code in
>> ccp4.setup-sh:
>>
>> if [ `expr ":${PATH}:" : ".*:${dir}:"` -eq 0 ]; then if test
>> $ccp4_first_in_path -eq 1; then PATH=${dir}:${PATH} else
>> PATH=${PATH}:${dir} fi fi
>>
>> Ignore the 'ccp4_first_in_path' business, unless the user has
>> hacked the script it always takes the 'then' clause of the 'if' so
>> it's actually doing this:
>>
>> if [ `expr ":${PATH}:" : ".*:${dir}:"` -eq 0 ]; then if test
>> $ccp4_first_in_path -eq 1; then PATH=${dir}:${PATH} fi fi
>>
>> So what happens is that the first time you source the setup for
>> v6.4 it prepends the directories for that version. If you then
>> source the setup for v6.3 it prepends the directories for that and
>> you will use the v6.3 executables. So far so good. Now what
>> happens if you source the setup for v6.4 again? The code above
>> ensures that the v6.4 directory is NOT prepended again and so it
>> will continue to use v6.3 until you logout & in again & reset the
>> path.
>>
>> Cheers
>>
>> -- Ian
>>
>>
>>
>>
>>
>>
>>
>> On 28 April 2014 14:54, Harry Powell <[log in to unmask]>
>> wrote:
>>
>> Hi Sreetama
>>
>> That's the problem - sourcing the old ccp4 6.3 distro has set up
>> MOSFLM_EXEC to point to an old copy of ipmosflm that will not run
>> with the latest iMosflm.
>>
>> Mosflm version 7.0.9 for Image plate and CCD data 14th May
>> 2012
>>
>>
>> which cannot be used with iMosflm 7.1.0.
>>
>> So it looks like there might be an issue with the ccp4 6.4 setup
>> not over-writing the environment variable MOSFLM_EXEC as it
>> should. The immediate way round this would be to not source ccp4
>> 6.3 in any terminal that you want to run iMosflm from.
>>
>> Can you send me & [log in to unmask] (*not* to the ccp4bb, please)
>> the output of
>>
>> echo $PATH which $MOSFLM_EXEC
>>
>> (1) before you "source ccp4-6.3" (2) after you "source ccp4-6.3"
>> (3) after you "source ccp4-6.4"
>>
>> So that we can get a clear idea of what is happening to your PATH
>> when you do each of these three things.
>>
>> On 28 Apr 2014, at 14:38, sreetama das wrote:
>>
>> Dear Sir, If I sorce ccp4-6.3, and then change in the bashrc
>> file &
>>
>> source ccp4-6.4, (and source the modified .bashrc file in either
>> case) but don't close the previous terminal, then opening imosflm
>> gives the aforementioned error. After closing the imosflm GUI, if
>> I type at the terminal, I get the following:
>>
>>
>> sreetama@sreetama-laptop:~/data $ $MOSFLM_EXEC <B><FONT
>> COLOR="#FF0000"><!--SUMMARY_BEGIN--> <html> <!-- CCP4 HTML
>> LOGFILE --> <hr> <!--SUMMARY_END--></FONT></B>
>>
>>
>> ************ Mosflm version 7.0.9 for Image plate and CCD data
>> 14th
>>
>> May 2012 ***********
>>
>> Andrew Leslie and Harry Powell, MRC Laboratory of Molecular
>> Biology, Hills Road, Cambridge CB2 0QH, UK E-mails:
>> [log in to unmask], [log in to unmask] References:
>> Mosflm: A.G.W. Leslie and H.R. Powell (2007), Evolving Methods
>> for Macromolecular Crystallography, 245, 41-51 ISBN
>>
>> 978-1-4020-6314-5
>>
>> New auto-indexing based on DPS: I. Steller R. Bolotovsky and
>> M.G.
>>
>> Rossmann
>>
>> (1997) J. Appl. Cryst. 30, 1036-1040 New iMosflm GUI: T.G.G.
>> Battye, L. Kontogiannis, O. Johnson, H.R.
>>
>> Powell
>>
>> and A.G.W. Leslie.(2011) Acta Cryst. D67, 271-281)
>>
>>
>> --------------------------------------------------------------------------------
>>
>>
>>
>> How much of this information is useful in diagnosing user problems?
>>
>> Mosflm run on Monday, April 28 2014 at 19:01 by sreetama
>> Compiler command: gfortran Compiler version: GNU Fortran (GCC)
>> 4.4.7 Copyright (C) 2010 Free
>>
>> Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to
>> the extent permitted by law. You may redistribute copies of GNU
>> Fortran under the terms of the GNU General Public License. For
>> more informatio
>>
>> Executable type: ELF 32-bit LSB executable, Intel 80386,
>> version
>>
>> 1 (SYSV), dynamically linked (uses shared libs), not stripped
>>
>> This executable was built by ccb on Thursday, June 28 2012 at
>> 09:33
>>
>>
>> --------------------------------------------------------------------------------
>>
>>
>>
>> MOSFLM =>
>>
>>
>> Also the terminal refuses to close if I type exit. Forcibly
>> closing the
>>
>> terminal , and typing imosflm in a new terminal solves the
>> problem.
>>
>> regards, sreetama On Monday, 28 April 2014 6:52 PM, Harry
>> Powell <[log in to unmask]>
>>
>> wrote:
>>
>> Hi
>>
>> When you get this error, and "everything" has been closed, what
>> do you
>>
>> get if you type (in the same terminal window that you tried to
>> start iMosflm) -
>>
>>
>> $MOSFLM_EXEC
>>
>> ?
>>
>> It's plain from the message that
>>
>> "ipmosflm" is not compatible'
>>
>> that iMosflm is trying to run with an incompatible MOSFLM_EXEC
>> (maybe
>>
>> from the old ccp4 6.3 distribution, but there could be other
>> reasons).
>>
>>
>> On 28 Apr 2014, at 13:05, sreetama das wrote:
>>
>> Dear All, Whenever I open up imosflm GUI from the terminal, I
>> get
>>
>> the following error:
>>
>>
>> iMosflm version 7.1.1, 24th March 2014 "ipmosflm" is not
>> compatible. Please configure iMosflm with the correct
>> executable.
>>
>> clicking the Configure button at the bottom of the error
>> message panel
>>
>> closes everything.
>>
>> the following is shown on the terminal:
>>
>> MOSFLM_EXEC set to ipmosflm testing MOSFLM_WISH
>> (/home/*****/Software/CCP4/ccp4-6.3.0/bin/wish) Tcl platform
>> is unix i686 Linux 3.8.0-32-generic TclTk version from info
>> patchlevel is 8.4.19 Tk windowing system is x11
>>
>>
>> I had run imosflm successfully just 2 hours before this
>> instance.
>>
>> After that, I had enabled the older version of CCP4-6.3 (by
>> sourcing it from the .bashrc file) for sometime to look at the
>> options in molrep (in CCP4-6.3), and then re-enabled the newer
>> CCP4-6.4.
>>
>> Enabling ccp4-6.3 from the .bashrc file & typing imosflm
>> opens up the
>>
>> older 7.0.1 version.
>>
>>
>> The option "settings>environment variables" is not working in
>> the
>>
>> newer imosflm version now, changing the value in the GUI of the
>> older version of imosflm doesn't help either.
>>
>> I applied the latest CCP4 updates; that doesn't set things
>> right.
>>
>> Please let me know how to re-configure iMosflm to run with
>> ccp4-6.4.
>>
>> thanks & regards, sreetama
>>
>>
>>
>> Harry -- ** note change of address ** Dr Harry Powell, MRC
>> Laboratory of Molecular Biology, Francis Crick
>>
>> Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH
>>
>> Chairman of European Crystallographic Association SIG9
>> (Crystallographic
>>
>> Computing)
>>
>>
>>
>> Harry -- ** note change of address ** Dr Harry Powell, MRC
>> Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge
>> Biomedical Campus, Cambridge CB2 0QH Chairman of European
>> Crystallographic Association SIG9 (Crystallographic Computing)
>>
>>
>>
>> - --
>> - --
>> Dr Tim Gruene
>> Institut fuer anorganische Chemie
>> Tammannstr. 4
>> D-37077 Goettingen
>>
>> GPG Key ID = A46BEE1A
>>
>> -----BEGIN PGP SIGNATURE-----
>> Version: GnuPG v1.4.12 (GNU/Linux)
>> Comment: Using GnuPG with Icedove - http://www.enigmail.net/
>>
>> iD8DBQFTXntDUxlJ7aRr7hoRAsiWAJ9wwKHzobUF26bMBDhfDuscVlK8PACeNbPT
>> F258uWzZSiod7h8s25Ajook=
>> =RmV/
>> -----END PGP SIGNATURE-----
>>
>>
>>
>
