[ccp4bb] HKL2MAP .sca files...
Hi folks When I run hkl2map for SAD data using unmerged .sca files produced by Aimless, I am invariably bugged by the fact that merged .sca files (from Aimless) have the unit cell in the first few lines, but the unmerged files don't - so I have to either type in the cell dimensions or (usually) read in the merged file to get the cell dimensions then read in the unmerged file to get the data that SHELXC really wants. So I'm wondering - what's the reasoning behind including the cell dimensions in the merged file and omitting them in the unmerged file? Would it break anything if the cell dimensions were included in the unmerged file? 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)
[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
[ccp4bb] LAST CALL -- New Schrodinger Workshop -- SBGrid/NE-CAT Computing School at Harvard
Only a few days left to register for Quo Vadis Structural Biology 2014. We've added Phenix and Schrodinger workshops in addition to our Data Processing Computing School. Visit the SBGrid website for the complete program https://sbgrid.org/news/sbgridne-cat-computing-school. *Quo Vadis Structural Biology 2014* SBGrid/NE-CAT Computing School June 5-7, 2014 Harvard Medical School -- Boston, MA *Registration Deadline: May 7, 2014* *Data Processing in Crystallography - June 5-6:* Speakers: Kay Diederichs, Phil Evans, Zbyszek Otwinowski, Jim Pflugrath, Dominika Borek, Piotr Sliz, Matt Benning, , Frank Murphy, David Neau, K. Rajashankar, Nick Sauter, Jon Schuermann, Clemens Schulze-Briese *Advances in Structure Determination with Phenix * Paul Adams Nathaniel Echols, Lawrence Berkeley National Laboratory Tom Terwilliger, Los Alamos National Laboratory *Improved Structural Modeling Using BioLuminate * Melissa Landon, Ph.D., Schrodinger, Inc. Complete meeting details can be found here: https://sbgrid.org/news/sbgridne-cat-computing-school *Additional Deadlines:* - *Lodging - May 4th: * We have a block of rooms reserved at the Inn at Longwood for a reduced rate through May 4th. After May 4th these rooms will be released to the general public and, due to graduations and the budding tourist season, it may become difficult to find a room near the meeting site. - *Poster Registration - May 7th: * We have extended the deadline to register for the poster session by one week. We need a final count for planning purposes, so if you wish to present a poster at our June 5th poster session, please REGISTER HEREhttps://docs.google.com/forms/d/1cvfQUWw5oZgN_e5q2BYapLsE_0Rq3xFrT0Inmip7nvU/viewform .
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),
Re: [ccp4bb] [PyMOL] Farewell
Jason - I’d also like to express my appreciation for all you’ve done to benefit the PyMOL community. You have, time and again, proven yourself to be an extremely responsive and helpful leader both in developing the software and in enabling others to learn to use it. Like many on these lists, I’m sure, after hearing of Warren’s untimely passing 5 years ago, I was saddened of course, but also concerned about what would happen to PyMOL without him. Fortunately, it couldn’t have landed in better hands. I wish you all the best in your new endeavor. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Apr 24, 2014, at 9:29 AM, Thomas Holder thomas.hol...@schrodinger.commailto:thomas.hol...@schrodinger.com wrote: Dear Jason, thank you so much for you deep commitment and your invaluable contributions to PyMOL and the PyMOL community. You assumed responsibility for PyMOL and managed to give it a new home at Schrödinger. We are sorry to see you leave and will truly miss you here. To me personally, you have been a great mentor and guide and I can hardly enumerate what I learned from you. I owe you deep gratitude. It is my honour to now take the lead on PyMOL and serve the community and our sponsors as best as I can. The PyMOL team at Schrödinger is strongly dedicated to continuously improve PyMOL and keep the PyMOL spirit alive. Cheers, Thomas On 24 Apr 2014, at 05:00, Jason Vertrees jason.vertr...@gmail.commailto:jason.vertr...@gmail.com wrote: Greetings PyMOLers and CCP4ers worldwide, It has been my great pleasure to serve the PyMOL community both in a volunteer and professional capacity for the past decade. I have recently been given an offer I can't refuse—to follow one of my dreams—helping lead technology and science at a new startup. March 30th marked my last day at Schrödinger and supporting PyMOL. Because of my great fondness for PyMOL and its community, I will continue to operate the PyMOLWiki until I find it a suitable home. I started the PyMOLWiki in 2005 and since then it's been visited over 15,289,590 times! (If you would like to sponsor or host the wiki feel free to email me.) Now I can't imagine the PyMOL community without it. Last, I am truly humbled to have followed in the footsteps of Warren DeLano. He was an amazing man whose ideas and actions have touched the lives of millions, whether they know it or not. He is missed. It's been great fun. I wish you all the best. Cheers, -- Jason -- Jason Vertrees, PhD (e) jason.vertr...@gmail.commailto:jason.vertr...@gmail.com (o) +1 (603) 374-7120 -- Thomas Holder PyMOL Developer Schrödinger, Inc. This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
[ccp4bb] TEV protease alternatives and Proteases which leave little on new C-term
Dear Crystallographers (this may be off-topic, depending on whom you ask...) A: Can anyone recommend new improved alternatives to the usual suspects for proteases (TEV, thrombin, enterokinase, etc.)? I've seen some literature about SUMO- and NEDD8-dependent enzymes, but those apparently require the whole protein domain to be in the construct for cleavage to happen, rather than just a short sequence motif. Further, I'd be curious whether there be drawbacks to using the various new breeds that might not be mentioned in the original publications thereon. B: While I have seen several proteases that leave behind only 1 aa on the new n-terminus of the target, I've yet to come across proteases that leave behind very few residues on the new c-terminus, which would be very helpful for tagging cleanly the c-terminus of proteins. Do such enzymes exist, and if so, are there particularly good ones? And if not, I wonder why proteases usually require more sequence on the n-terminal side of the scissile bond? All the best, Jacob Keller *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***
Re: [ccp4bb] TEV protease alternatives and Proteases which leave little on new C-term
Dear Jacob, We have been using factor XA for several years for tag removal of the proteins we express in the facility. Factor XA does not leave an overhang, cutting after an IEGR sequence. It can be quite expensive though so we are looking into methods to purify it from bovine plasma. David Blum Bioexpression and Fermentation Facility University of Georgia b...@uga.edu bff.uga.edu On Mon, Apr 28, 2014 at 3:01 PM, Keller, Jacob kell...@janelia.hhmi.orgwrote: Dear Crystallographers (this may be off-topic, depending on whom you ask...) A: Can anyone recommend new improved alternatives to the usual suspects for proteases (TEV, thrombin, enterokinase, etc.)? I've seen some literature about SUMO- and NEDD8-dependent enzymes, but those apparently require the whole protein domain to be in the construct for cleavage to happen, rather than just a short sequence motif. Further, I'd be curious whether there be drawbacks to using the various new breeds that might not be mentioned in the original publications thereon. B: While I have seen several proteases that leave behind only 1 aa on the new n-terminus of the target, I've yet to come across proteases that leave behind very few residues on the new c-terminus, which would be very helpful for tagging cleanly the c-terminus of proteins. Do such enzymes exist, and if so, are there particularly good ones? And if not, I wonder why proteases usually require more sequence on the n-terminal side of the scissile bond? All the best, Jacob Keller *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***
[ccp4bb] Problem with Rfactor
Dear All, I am very new to the field of crystallography, I have a few questions which are very basic and getting input from this forum would help me a lot. Firstly I am trying to solve a structure using MR Molrep. In the result the Rfactors are really high how do I reduce the same?? ..When I tried with Phaser I didnt get any solution at all.. Will der be a problem with the space group?? like the model is in monoclinic and the data which I have is processed in hexagonal. Secondly while using hexagonal space group should I search for only one monomer in Molrep?? These are very basic questions if anybody could help me out with this , I would be very happy for the same. Sudarshan .N. Murthy Crystallography Division Bangalore
