Re: [ccp4bb] error in starting imosflm
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I remember reading somewhere that 6.3.0 version is obsolete.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: mbfro...@post.tau.ac.il
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Apr 28, 2014, at 19:01 , Tim Gruene t...@shelx.uni-ac.gwdg.de 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 ha...@mrc-lmb.cam.ac.uk
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 c...@stfc.ac.uk (*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 BFONT
COLOR=#FF!--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:
and...@mrc-lmb.cam.ac.uk, ha...@mrc-lmb.cam.ac.uk 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
Re: [ccp4bb] error in starting imosflm
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 $CEXAM) for users to test the software (though the examples there
are hardly comprehensive). Most major software packages (e.g. LAPACK)
provide comprehensive test suites that test all possible ways in which the
software may be used so you can verify that the new version at least gives
the same results as the distributor's test suite (this also checks whether
there are machine dependencies). So I need to run tests on the new version
compare with results from the old one before I release it to users, for
which I obviously need access to both versions. Also the man pages are
missing from the new version: I just find it quicker easier to type 'man
fft' or whatever than to fire up the browser.
Cheers
-- Ian
On 29 April 2014 11:23, Felix Frolow mbfro...@post.tau.ac.il wrote:
Hi Tim,
What can be a reason to work with an obsolete version of CCP4?
I remember reading somewhere that 6.3.0 version is obsolete.
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of
Molecular Microbiology and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail: mbfro...@post.tau.ac.il
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Apr 28, 2014, at 19:01 , Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Sreetama, dear Ian,
I avoid sourcing both version 6.3 and 6.4 in the same terminal. If I
need to work with 6.3 I modify my .bashrc from 6.4 to 6.3 and then
open a new terminal to make sure everything refers to v6.3 and vice versa.
Best,
Tim
On 04/28/2014 04:51 PM, Ian Tickle wrote:
Harry,
I've run into this problem before with other programs when I switch
between v6.3 v6.4. I think the problem is this code in
ccp4.setup-sh:
if [ `expr :${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 ha...@mrc-lmb.cam.ac.uk
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 c...@stfc.ac.uk (*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 $ $MOSFLM_EXEC BFONT
COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML
LOGFILE -- hr !--SUMMARY_END--/FONT/B
Mosflm version 7.0.9 for Image plate and CCD data
14th
May 2012 ***
Andrew Leslie and Harry Powell, MRC Laboratory of Molecular
Biology, Hills Road, Cambridge CB2 0QH, UK E-mails:
and...@mrc-lmb.cam.ac.uk, ha...@mrc-lmb.cam.ac.uk References:
Mosflm: A.G.W. Leslie and H.R. Powell (2007), Evolving Methods
for Macromolecular Crystallography, 245, 41-51 ISBN
978-1-4020-6314-5
New auto-indexing based on DPS: I. Steller R. Bolotovsky and
M.G.
Rossmann
(1997) J. Appl. Cryst. 30, 1036-1040 New
Re: [ccp4bb] error in starting imosflm
On Mon, Apr 28, 2014 at 03:51:57PM +0100, Ian Tickle wrote:
Harry,
I've run into this problem before with other programs when I switch between
v6.3 v6.4. I think the problem is this code in ccp4.setup-sh:
if [ `expr :${PATH}: : .*:${dir}:` -eq 0 ]; then
We can remove this condition if it does more harm than good.
Marcin
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are not the intended addressee or an authorised recipient of the addressee
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments
are free from viruses and we cannot accept liability for any damage which you
may sustain as a result of software viruses which may be transmitted in or with
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and
Wales with its registered office at Diamond House, Harwell Science and
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] error in starting imosflm
Hi Marcin
It was obviously added originally because there was a limit to the length
of the PATH variable (presumably there still is), so repeated invocations
of setup scripts could take you over the limit. Ideally the script should
remove old versions from the PATH, not just prepend the new one, but
there's no easy way to make that completely general. David's
CCP4Dispatchers script would seem to offer the best solution.
So I would leave it as it is, the cure may be worse than the disease!
Thanks
-- Ian
On 29 April 2014 12:47, Marcin Wojdyr marcin.woj...@diamond.ac.uk wrote:
On Mon, Apr 28, 2014 at 03:51:57PM +0100, Ian Tickle wrote:
Harry,
I've run into this problem before with other programs when I switch
between
v6.3 v6.4. I think the problem is this code in ccp4.setup-sh:
if [ `expr :${PATH}: : .*:${dir}:` -eq 0 ]; then
We can remove this condition if it does more harm than good.
Marcin
--
This e-mail and any attachments may contain confidential, copyright and or
privileged material, and are for the use of the intended addressee only. If
you are not the intended addressee or an authorised recipient of the
addressee please notify us of receipt by returning the e-mail and do not
use, copy, retain, distribute or disclose the information in or attached to
the e-mail.
Any opinions expressed within this e-mail are those of the individual and
not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any
attachments are free from viruses and we cannot accept liability for any
damage which you may sustain as a result of software viruses which may be
transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England
and Wales with its registered office at Diamond House, Harwell Science and
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] error in starting imosflm
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 ianj...@gmail.com 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 $CEXAM) for users to test the software (though the examples there
are hardly comprehensive). Most major software packages (e.g. LAPACK)
provide comprehensive test suites that test all possible ways in which the
software may be used so you can verify that the new version at least gives
the same results as the distributor's test suite (this also checks whether
there are machine dependencies). So I need to run tests on the new version
compare with results from the old one before I release it to users, for
which I obviously need access to both versions. Also the man pages are
missing from the new version: I just find it quicker easier to type 'man
fft' or whatever than to fire up the browser.
Cheers
-- Ian
On 29 April 2014 11:23, Felix Frolow mbfro...@post.tau.ac.il wrote:
Hi Tim,
What can be a reason to work with an obsolete version of CCP4?
I remember reading somewhere that 6.3.0 version is obsolete.
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of
Molecular Microbiology and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail: mbfro...@post.tau.ac.il
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Apr 28, 2014, at 19:01 , Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Sreetama, dear Ian,
I avoid sourcing both version 6.3 and 6.4 in the same terminal. If I
need to work with 6.3 I modify my .bashrc from 6.4 to 6.3 and then
open a new terminal to make sure everything refers to v6.3 and vice versa.
Best,
Tim
On 04/28/2014 04:51 PM, Ian Tickle wrote:
Harry,
I've run into this problem before with other programs when I switch
between v6.3 v6.4. I think the problem is this code in
ccp4.setup-sh:
if [ `expr :${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 ha...@mrc-lmb.cam.ac.uk
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 c...@stfc.ac.uk (*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 BFONT
COLOR=#FF!--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
[ccp4bb] error in starting imosflm
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 settingsenvironment 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
Re: [ccp4bb] error in starting imosflm
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 settingsenvironment 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)
Re: [ccp4bb] error in starting imosflm
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 BFONT COLOR=#FF!--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: and...@mrc-lmb.cam.ac.uk, ha...@mrc-lmb.cam.ac.uk 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 ha...@mrc-lmb.cam.ac.uk 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 settingsenvironment 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)
Re: [ccp4bb] error in starting imosflm
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 c...@stfc.ac.uk (*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 BFONT COLOR=#FF!--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: and...@mrc-lmb.cam.ac.uk, ha...@mrc-lmb.cam.ac.uk 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 ha...@mrc-lmb.cam.ac.uk 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) - $MOSFLM_EXEC ? It's plain from the message that ipmosflm is not compatible' that iMosflm is trying to run with an incompatible MOSFLM_EXEC (maybe from the old ccp4 6.3 distribution, but there could be other reasons). On 28 Apr 2014, at 13:05, sreetama das wrote: Dear All, Whenever I open up imosflm GUI from the terminal, I get the following error: iMosflm version 7.1.1, 24th March 2014 ipmosflm is not compatible. Please configure iMosflm with the correct executable. clicking the Configure button at the bottom of the error message panel closes everything. the following is shown on the terminal: MOSFLM_EXEC set to ipmosflm testing MOSFLM_WISH (/home/*/Software/CCP4/ccp4-6.3.0/bin/wish) Tcl platform is unix i686 Linux 3.8.0-32-generic TclTk version from info patchlevel is 8.4.19 Tk windowing system is x11 I had run imosflm successfully just 2 hours before this instance. After that, I had enabled the older version of CCP4-6.3 (by sourcing it from the .bashrc file) for sometime to look at the options in molrep (in CCP4-6.3), and then re-enabled the newer CCP4-6.4. Enabling ccp4-6.3 from the .bashrc file typing imosflm opens up the older 7.0.1 version. The option settingsenvironment variables is not working in the newer imosflm version now, changing the value in the GUI of the older version of imosflm doesn't help either. I applied the latest CCP4 updates; that doesn't set things right. Please let me know how to re-configure iMosflm to run with ccp4-6.4. thanks regards, sreetama Harry -- ** note change
Re: [ccp4bb] error in starting imosflm
Harry,
I've run into this problem before with other programs when I switch between
v6.3 v6.4. I think the problem is this code in ccp4.setup-sh:
if [ `expr :${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 ha...@mrc-lmb.cam.ac.uk 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 c...@stfc.ac.uk (*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
BFONT COLOR=#FF!--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: and...@mrc-lmb.cam.ac.uk, ha...@mrc-lmb.cam.ac.uk
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 ha...@mrc-lmb.cam.ac.uk
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) -
$MOSFLM_EXEC
?
It's plain from the message that
ipmosflm is not compatible'
that iMosflm is trying to run with an incompatible MOSFLM_EXEC (maybe
from the old ccp4 6.3 distribution, but there could be other reasons).
On 28 Apr 2014, at 13:05, sreetama das wrote:
Dear All,
Whenever I open up imosflm GUI from the terminal, I get
the following error:
iMosflm version 7.1.1, 24th March 2014
ipmosflm is not
Re: [ccp4bb] error in starting imosflm
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Sreetama, dear Ian,
I avoid sourcing both version 6.3 and 6.4 in the same terminal. If I
need to work with 6.3 I modify my .bashrc from 6.4 to 6.3 and then
open a new terminal to make sure everything refers to v6.3 and vice versa.
Best,
Tim
On 04/28/2014 04:51 PM, Ian Tickle wrote:
Harry,
I've run into this problem before with other programs when I switch
between v6.3 v6.4. I think the problem is this code in
ccp4.setup-sh:
if [ `expr :${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 ha...@mrc-lmb.cam.ac.uk
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 c...@stfc.ac.uk (*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 BFONT
COLOR=#FF!--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:
and...@mrc-lmb.cam.ac.uk, ha...@mrc-lmb.cam.ac.uk 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 ha...@mrc-lmb.cam.ac.uk
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
Re: [ccp4bb] error in starting imosflm
Dear all,
For experiments that involve switching between different versions of CCP4
you might like to try the CCP4Dispatchers scripts (see
http://www.ccp4.ac.uk/html/CCP4Dispatchers.html). On a binary install of
ccp4 6.4.0 these will have been generated automatically. For example, on my
Linux machine typing
/path/to/ccp4-6.4.0/share/python/CCP4Dispatchers/bin/imosflm starts imosflm
without anything needed to be sourced in the terminal beforehand. Of course
this is more useful if dispatchers are also generated for the other
versions of CCP4 you want to use. There are some instructions for doing
that in the link above, and the files you need are located in $CCP4/libexec
of a ccp4-6.4.0 install.
Cheers
-- David
On 28 April 2014 17:01, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Sreetama, dear Ian,
I avoid sourcing both version 6.3 and 6.4 in the same terminal. If I
need to work with 6.3 I modify my .bashrc from 6.4 to 6.3 and then
open a new terminal to make sure everything refers to v6.3 and vice versa.
Best,
Tim
On 04/28/2014 04:51 PM, Ian Tickle wrote:
Harry,
I've run into this problem before with other programs when I switch
between v6.3 v6.4. I think the problem is this code in
ccp4.setup-sh:
if [ `expr :${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 ha...@mrc-lmb.cam.ac.uk
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 c...@stfc.ac.uk (*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 BFONT
COLOR=#FF!--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:
and...@mrc-lmb.cam.ac.uk, ha...@mrc-lmb.cam.ac.uk 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),
