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On Aug 24, 2009, at 5:30 PM, Ethan Merritt wrote:
Not sure this is the right place to ask, but...
I'm trying to chain some ccp4 programs together via a script.
It creates temporary files with arbitrary names based on the process
id.
The problem is that when I try to pass one of these files
You should be able to do this kind of scripting.
The CCP4 library will try to add an extension, iff there is not one
already. But if you have set $tempfile to foo.pdb then it shouldn't
add anything.
Code is in ccp4_general.c if you want to sabotage it ...
The list of default extensions is in
Dear all,
Sorry for the non-ccp4 question. Recently I have got some long needle of on
35 kDa protein with 65% MPD at 4 degree C at pH 3.6 (50 mM NaOAc buffer).
The protein contains 50mM of salt. The florets are very thin. I need some
suggestions regarding the optimization of the crystallization
Hi,
I am running CCP4 version ccp4-6.1.1 on Mac OS X. I was working
without any problems until the gui crashed and when I tried to start
it up again it lost my PROJECT directory information. I restarted the
computer and now I can't even get the gui up, if flashes up for a
second and
James and those that may be interested,
65% MPD at 4 degree C at pH 3.6 are conditions that stimulate the growth
of salt crystals, but one cannot exclude that the florets are indeed
protein.
1. If you are sure you are dealing with protein crystals try the
co-precipitant
approach: Carry out a
Hi Atlanta-
Yep, this one bit me (on Mac OS X), too. To fix it, I had to go to
/usr/local/ccp4-6.1.2/share/ccp4i/etc/UNIX and edit my configure.def file.
Almost at the end of the file, there is a line that says
USE_DBCCP4I_ON_STARTUP. Change the value from 1 to 0. This should
refresh your project
Hi
Thanks for the various suggestions. It turns out that I can get rid
of the error by deleting the file ~/.CCP4/unix/status.def.
Atlanta
On 25 Aug 2009, at 16:29, Brad Bennett wrote:
Hi Atlanta-
Yep, this one bit me (on Mac OS X), too. To fix it, I had to go to /
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On Tuesday 25 August 2009 01:27:52 Martyn Winn wrote:
You should be able to do this kind of scripting.
The CCP4 library will try to add an extension, iff there is not one
already. But if you have set $tempfile to foo.pdb then it shouldn't
add anything.
Since several people have expressed
Hi Ethan,
On Tue, Aug 25, 2009 at 09:21:01AM -0700, Ethan Merritt wrote:
mv $1 $1.brk
...
That works, but at the cost of an unnecessary file copy operation.
That is just a rename operation, right? So I doubt it has any major
overhead (but might be wrong). or
% ln -s $1 $1.pdb
instead?
As Clemens said, the mv simply renames, shouldn't copy any data,
so should be ok. I would say that is a perfectly valid thing
to do in a script, and not just a workaround.
If you look in ccp4_general.c, IIRC it is function ccp4setenv, and
there is a comment (sic!) that says something like add
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But now I want to run the script from a cgi script as part of the
processing by a web service. No matter what the name of the file
that was originally uploaded, the web server has homogenized it to
a local temporary file whose name is generated by a hash function
from the pid. The cgi script
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