Re: [ccp4bb] problems about installation of mosflm701
Hi
First off, you really shouldn't be installing mosflm version 7.0.1 -
version 7.0.3 is the current one, and contains numerous bug fixes.
The developers are likely to meet any problem queries relating to
7.0.1 with update to the current version first, then try again; if
the problem persists, we will look at it...
Your immediate problem is that you are trying to run a csh script as
a bash script, without editing the file properly; e.g., you can't
just change setenv (csh) to export (bash) - the syntax is not the
same - you'd need to change it thus -
setenv CCP4_LIB_FILES '-lccp4f -lccp4c -lxdl_view'
would become something like
export CCP4_LIB_FILES='-lccp4f -lccp4c -lxdl_view'
You would also need to change the top line of the file so that it was
something like #!/bin/bash -f, though I would be more inclined to
use a proper traditional Bourne shell for this and use #!/bin/sh -f
and use sets and exports throughout.
If you really want to run the script, I would use tcsh or csh, rather
than trying to modify it so that it is a bash script.
BTW, the Intel compiler setup in that file is way out of date - you'd
need to change that as well to point to current copies of the compilers.
I would be very strongly inclined to install the mosflm_linux_suse
pre-built executable - it should certainly work on FC5, and saves you
the trouble of trying to build it. The speedup by using an executable
compiled with the Intel compiler is probably not that great - recent
g77s and gfortrans give excellent and stable optimization!
On 27 Mar 2008, at 04:57, Lu Yongzhi wrote:
- Original Message -
From: Lu Yongzhi
To: ccp4 bb
Sent: Wednesday, March 26, 2008 7:41 PM
Subject: problems about installation of mosflm701
Hi,
My OS is fedoral core 5. I have installed ccp4-6.0.2 which include
the mosflm 6, but I want to install mosflm7.0.1. I downloaded the
program, but I can't install it properly. I source the file
'intel', the echo is (I have changed the 'setenv' to 'export'):
bash: export: `-lccp4f -lccp4c -lxdl_view': not a valid identifier
MOSROOT has been set to
bash: export: `/index': not a valid identifier
bash: export: `/src/dps/util': not a valid identifier
bash: export: `/jpg': not a valid identifier
bash: intel: line 65: syntax error: unexpected end of file
could anyone can help me.
the lines in the 'intel' file are:
#!/bin/csh -fv
#
# setup shell script for the development copies of Mosflm for
different
# platforms.
#
# Common stuff first
#
export CCP4_LIB_FILES '-lccp4f -lccp4c -lxdl_view'
set mosroot = ${cwd:h}
export MOSROOT $mosroot
echo MOSROOT has been set to $MOSROOT
set moshome = ${cwd}
export MOSHOME $moshome
echo $MOSHOME
export AR_FLAGS vru
export DPS ${MOSHOME}
export IND ${MOSHOME}/index
export UTIL${MOSHOME}/src/dps/util
export JPG ${MOSHOME}/jpg
# intel compiler specifics - change this to your local installation
if ( -e /opt/intel/compiler70/ia32/bin/ifcvars.csh )then
source /opt/intel/compiler70/ia32/bin/ifcvars.csh
else
echo You must either edit the file called \intel\ to source
the correct
echo ifcvars.csh file or install both the Intel C++ and FORTRAN
compilers
exit
endif
if ( -e /opt/intel/compiler70/ia32/ifc_fudge.o )then
export FUDGE /opt/intel/compiler70/ia32/ifc_fudge.o
export NOFUDGE
else
export FUDGE
export NOFUDGE -i_dynamic
endif
export DEBUG
export F77 ifc ${DEBUG}
export FCOMP ${F77}
export FC ${F77}
export CC icc ${DEBUG}
export FLINK ${F77} ${DEBUG}
export FFLAGS -O -align -w90 -cm
export CFLAGS -O0 -O -DPROTOTYPE -DIFC -c -w
# if no fudge.o vide infra export LFLAGS-Vaxlib -i_dynamic
export LFLAGS-Vaxlib $NOFUDGE
#
# (2) Mosflm directory
#
export MOSFLAGS -O3 -align -w90 -cm
# export MOSFLAGS -O3 -align -w90 -cm -prof_gen this line for
profiling only
# export MOSFLAGS -O3 -align -w90 -cm -prof_use change $F77
etc to include -ipo flag
export MCFLAGS -O0
export MOSLIBS -L${CCP4_LIB} ${CCP4_LIB_FILES} -lncurses -L/
usr/X11R6/lib -lXt -lSM -lICE -lX11 -ldl -lpthread -lm ${FUDGE}
#
# (3) CBF directories
#
export CBFCFLAGS -O -DPROTOTYPE -DIFC
# DPS
export VERBOSE v
export UTILFLAGS -O -DPROTOTYPE -DIFC -c -w
export EXTRAFLAGS -I${UTIL}
export STDCFLAGS
exit
Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,
Hills Road, Cambridge, CB2 2QH
Re: [ccp4bb] problems about installation of mosflm701
You would also need to change the top line of the file so that it was something like #!/bin/bash -f, though I would be more inclined to use a proper traditional Bourne shell for this and use #!/bin/sh -f and use sets and exports throughout. That's not actually necessary for a 'sourced' script because 'source' reads it as a text file, not as an executable script, i.e. all you are doing is temporarily switching input for the *current* shell from the terminal to the file and back again. So the first line, whatever it is, if it begins with '#' it will be treated as a comment (that's why the '#' is put there!). In contrast, *running* a shell script starts a *new* (child) shell (which need not be the same shell as the parent shell). If you start it like so: 'shell script_name' the shell specified on the command line is used and any shell specification inside the script is ignored; whereas if you start it like so: 'script_name' (in which case it must be made executable first otherwise you will get 'permission denied'), then the shell specified by the first line '#!shell' is used (if the first line is not in this format it uses /bin/sh and the line is treated as a normal shell command). For a script which is intended to set up the environment for other programs (e.g. CCP4) it's essential to source the file so that the commands in the file modify the environment of the current shell from which you will launch the programs. If you run it in a child shell the environment set up for the child process is *not* passed back to the parent shell, so it will have absolutely no effect. I often see people *running* programs (i.e. not just setting up the environment) by sourcing a script, i.e. the script contains commands for running programs: I always think that's a dangerous thing to do because anything in the file which changes the environment will change the environment for the terminal shell you are using, with unpredictable consequences for things you type in later. If I do that accidentally I always immediately terminate the terminal shell and start a new one so that the shell is in a known state, just to be on the safe side. It's always safer to *run* programs with a shell script using 'shell script_name' or 'script_name' so then the script is completely isolated from the terminal shell. If you really want to run the script, I would use tcsh or csh, rather than trying to modify it so that it is a bash script. That's all very well but people use other shells for their terminal sessions for other reasons (e.g. csh/tcsh isn't guaranteed to be portable, or the user may already have setup scripts for their current shell which they don't want to rewrite). As indicated above the commands used in a 'sourced' script must correspond to the terminal shell, since it is that environment you want to modify: any shell specification inside the script is ignored, e.g. if you want to use bash for your terminal shell (many people do!) then the sourced file *must* contain bash commands, there's no way around it (this is why CCP4 supplies versions of the setup script for both sh and csh). Cheers -- Ian Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
[ccp4bb] OMIT map from Sfcheck
Dear, I'm intending to make an OMIT map using Sfcheck (ccp4i 6.0.2, Mac OS X Tiger, PPC). However, the program terminates with: has failed with error message 1525-005 1525-005 1525-005 1525-005 1525-005 1525-005 When using 'command line' from a script (with '-nomit 2 -map -origin - out y') I got: Last system error message: No such file or directory CCP4: Open failed: File: /Users/kristof/data/11mer/data2/ sfcheck_scr.dat Does anyone know this problem please..? Many thanks Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] expression vector
Hello,everyone! I have a question,is the expression vector effect crystallization much? For example,PQE2-protein structure has 2 molecules in one unit-cell,PQE70-protein single mutant has 5molecules in one unit-cell.Is the vector effect the results or the mutant itself? Can protein with some kind vector does not produce crystals? Thank you very much! Best wishes! liuqing _ Windows Live Photo gallery 数码相机的超级伴侣，轻松管理和编辑照片，还能制作全景美图！ http://get.live.cn/product/photo.html
[ccp4bb] Pointless 1.2.15 and ccp4i
Dear List, I am having a problem with running the latest version of pointless (1.2.15) via ccp4i. This is with the new GUI task. The logfile has the following, rather unhelpful information: SNIP *** * Information from CCP4Interface script *** The program run with command: pointless has failed with error message child killed: segmentation violation *** #CCP4I TERMINATION STATUS 0 child killed: segmentation violation #CCP4I TERMINATION TIME 27 Mar 2008 14:16:02 #CCP4I MESSAGE Task failed The program runs fine with the equivalent command line: pointless HKLIN Plate2_B6_001.mtz This is happening on both 32 and 64 bit linux machines, running either Fedora Core or SuSE. I have not, yet, recompiled the program from source, but that is next on the list. Has anyone else had this problem? Many thanks Andrew Purkiss-Trew
Re: [ccp4bb] expression vector
杨柳青 wrote: Hello,everyone! I have a question,is the expression vector effect crystallization much? For example,PQE2-protein structure has 2 molecules in one unit-cell,PQE70-protein single mutant has 5molecules in one unit-cell.Is the vector effect the results or the mutant itself? Can protein with some kind vector does not produce crystals? Thank you very much! Best wishes! liuqing 使用新一代 Windows Live Messenger 轻松交流和共享！ 立即体验！ http://messenger.live.cn/ The expression vector is essentially irrelevant to protein crystallization, as it is only the means by which the recombinant protein is produced. However, the protein structure does have everything to do with crystallization conditions and results. Single amino acid mutations, or the presence of purification tags, can have profound effects on the unit cell symmetry and size of protein crystals. In addition, a single protein can, and often does, crystallize under different crystallization conditions in wildly different space groups and asymmetric units. -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED]
Re: [ccp4bb] Pointless 1.2.15 and ccp4i
I've had some problems getting recent versions of Pointless to link in a portable way, due to a new call into the CCP4 library, this can cause segfaults on some systems. I keep hoping someone will tel me how to get round this (a ccp4 routine calls getpwid which apparently cannot be static) You could try ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.2.16.linux to see if that behaves better If it's going to crash, it will crash immediately on starting from the command line Phil On Thu, 2008-03-27 at 14:39 +, Andrew Purkiss-Trew wrote: Dear List, I am having a problem with running the latest version of pointless (1.2.15) via ccp4i. This is with the new GUI task. The logfile has the following, rather unhelpful information: SNIP *** * Information from CCP4Interface script *** The program run with command: pointless has failed with error message child killed: segmentation violation *** #CCP4I TERMINATION STATUS 0 child killed: segmentation violation #CCP4I TERMINATION TIME 27 Mar 2008 14:16:02 #CCP4I MESSAGE Task failed The program runs fine with the equivalent command line: pointless HKLIN Plate2_B6_001.mtz This is happening on both 32 and 64 bit linux machines, running either Fedora Core or SuSE. I have not, yet, recompiled the program from source, but that is next on the list. Has anyone else had this problem? Many thanks Andrew Purkiss-Trew
Re: [ccp4bb] Pointless 1.2.15 and ccp4i
Installation of pointless-1.2.16 appears to have solved the problem. On Thu, 2008-03-27 at 14:55 +, Phil Evans wrote: I've had some problems getting recent versions of Pointless to link in a portable way, due to a new call into the CCP4 library, this can cause segfaults on some systems. I keep hoping someone will tel me how to get round this (a ccp4 routine calls getpwid which apparently cannot be static) You could try ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.2.16.linux to see if that behaves better If it's going to crash, it will crash immediately on starting from the command line Phil On Thu, 2008-03-27 at 14:39 +, Andrew Purkiss-Trew wrote: Dear List, I am having a problem with running the latest version of pointless (1.2.15) via ccp4i. This is with the new GUI task. The logfile has the following, rather unhelpful information: SNIP *** * Information from CCP4Interface script *** The program run with command: pointless has failed with error message child killed: segmentation violation *** #CCP4I TERMINATION STATUS 0 child killed: segmentation violation #CCP4I TERMINATION TIME 27 Mar 2008 14:16:02 #CCP4I MESSAGE Task failed The program runs fine with the equivalent command line: pointless HKLIN Plate2_B6_001.mtz This is happening on both 32 and 64 bit linux machines, running either Fedora Core or SuSE. I have not, yet, recompiled the program from source, but that is next on the list. Has anyone else had this problem? Many thanks Andrew Purkiss-Trew
Re: [ccp4bb] expression vector
I agree with Roger - provided, of course, that the same protein is expressed from either vector with no extra amino acids at either end. Quite often vectors include extra sequence at the N or C terminus that are remnants of regions or linkers between the protein and purification tags. There are definitely cases where a few amino acids can make all the difference in crystallization. In addition there are vectors that contain solubility tags that, if they are not removed, might seriously impede crystallization. You seem lucky, though, since both versions crystallize. Good for you! Miles On Mar 27, 2008, at 7:55 AM, Roger Rowlett wrote: 杨柳青 wrote: polylinker Hello,everyone! I have a question,is the expression vector effect crystallization much? For example,PQE2-protein structure has 2 molecules in one unit-cell,PQE70-protein single mutant has 5molecules in one unit-cell.Is the vector effect the results or the mutant itself? Can protein with some kind vector does not produce crystals? Thank you very much! Best wishes! liuqing 使用新一代 Windows Live Messenger 轻松交流和共享！ 立即体验！ http://messenger.live.cn/ The expression vector is essentially irrelevant to protein crystallization, as it is only the means by which the recombinant protein is produced. However, the protein structure does have everything to do with crystallization conditions and results. Single amino acid mutations, or the presence of purification tags, can have profound effects on the unit cell symmetry and size of protein crystals. In addition, a single protein can, and often does, crystallize under different crystallization conditions in wildly different space groups and asymmetric units. -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED] Miles Pufall Postdoctoral Scholar Yamamoto Lab UC San Francisco Cellular and Molecular Pharmacology Mail Stop 2280 600 16th Street, Genentech Hall S-574 San Francisco, California 94158-2517 (415)476-4480
Re: [ccp4bb] expression vector
Hi,Yang, Tag(type and length) ,surface charge and crystallization condition are parameters which affect the packing in the crystal. It should be the tag or mutation not the the vector itself made you get different unit cell. ta liu 杨柳青 wrote: Hello,everyone! I have a question,is the expression vector effect crystallization much? For example,PQE2-protein structure has 2 molecules in one unit-cell,PQE70-protein single mutant has 5molecules in one unit-cell.Is the vector effect the results or the mutant itself? Can protein with some kind vector does not produce crystals? Thank you very much! Best wishes! liuqing 使用新一代 Windows Live Messenger 轻松交流和共享！ 立即体验！ http://messenger.live.cn/
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Hi All, I'm having trouble putting an EM map into a large P1 box for molecular replacement. We're trying to put density for a molecule about 300A in size into a 1000A P1 box. Using maprot in cutting mode with a mask yields a map with 1000A axes, but the extent of the map only covers part of the cell (not the whole 1000A box). Does anyone know how to do this? Thanks, Larry -- Lawrence Shapiro, Ph.D. Associate Professor Dept. of Biochemistry and Molecular Biophysics Jules and Doris Stein Professor of Research to Prevent Blindness Edward S. Harkness Eye Institute Columbia University 701 West 168th Street, 7th Floor New York, NY 10032 Tel: (212)342-6029 Fax: (212)342-6026 e-mail: [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.shapirolab.org
[ccp4bb] about Mosflm once more
Hello, Thank you very much for your help, now I setup Mosflm703 successfully. By the way, can I remove the ccp4 program suite including previous version and integrate the latest version into ccp4. Thanks Sincerely Lu Yongzhi
