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Hi there;
The 'problem' is that the ccp4i interface 'automatically' adds the
quoates around filenames, I guess because most CCP4i programs take
filenames on the command line and using quotes there makes a lot of
sense (to 'escape' special characters sometimes used in filenames).
In this case the quotes are 'removed' by the shell before the
arguments are passed to the program invoked.
Now the thing is that phaser takes the filenames on its standard
input, so it would be up to phaser to remove the quotes (if it wants
to handle this way), which is the case in the current version (1.3.2,
for some filenames but not for all its input), but might have been
different in previous versions ?
In particular, I discovered two days ago, that when you select (in
'additional parameters') PDB file output or MTZ file output to be on,
it will add the ON between quotes in the com file (you can check
using the 'run & view com file') which phaser chokes on. The solution
in this case is to modify a bit the file :
$CCP4I_TOP/templates/phaser_MR.com, and change these lines (73/74):
from :
< {$TOG_XYZOUT} XYZOUT \\"$XYZOUT_ONOFF\\"
< {$TOG_HKLOUT} HKLOUT \\"$HKLOUT_ONOFF\\"
to :
> {$TOG_XYZOUT} XYZOUT $XYZOUT_ONOFF
> {$TOG_HKLOUT} HKLOUT $HKLOUT_ONOFF
Also it looks like the '&' is what the input parser of phaser is
using to say that a line is continuing despite a newline.
Hope this is clear enough ...
Serge.
Le 15 déc. 06 à 17:09, William Scott a écrit :
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Hi Chris:
Sorry to do this, but I need to enlist the help of someone who
knows how
ccp4i works (I don't ever use it, so I am in a bad position to help,
although I do want to incorporate the fix).
So I am cc-ing this to the CCP4bb with the hope that someone with
one more
digit of IQ than I currently seem to possess can see the answer.
Bill
Chris Richardson wrote:
On 15 Dec 2006, at 15:37, William Scott wrote:
Thanks to the 8 hour time difference, I am just waking up, and this
is my pre-coffee response
That's dedication above and beyond the call of duty.
Is this directory string what you are using on OS X? If so, you
might just need to replace /home with /Users/username
Also, the & sign strikes me as weird, and because of the quotes,
that space between pdb and & is considered part of the filename.
Ah, I probably should have mentioned that all network account home
directories live in /home on our Macs. This is a consequence of
fitting them into an existing set of SGIs and Linux boxen with NFS-
mounted home directories and NIS for user authentication. Just in
case this is the cause of the problem (and it's the cause of most of
my problems) I tried it again with a local user. The user was a
local admin account, and everything was in its home directory (/
Users/
localadmin). The same problem arose.
I've checked the &, and it appears outside the quotes in the input to
phaser, so that should have been
PDBFILE "/path/to/some.pdb" &
I did a bit more fiddling. Even if only the mtz path is in quotes it
dies with the same error. I moved to the directory with the mtz
file and put just the filename instead of the full path. Again, it
died with quotes but not without. Then I noticed that the error
message includes the quotes around the filename. For example
----------------------------------------------------------------
FATAL RUNTIME ERROR: Cannot open MTZ file: "hex_P321_scala1.mtz"
----------------------------------------------------------------
I created a copy of the mtz file with quotes in its name using shell
escapes. Phaser ran without an error. It seems to be interpreting
the double quotes literally.
Chris
--
Dr Chris Richardson - sysadmin, Structural Biology Section, icr.ac.uk
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