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Hi Chris:
Can you verify that this solves the problem, and if it does, I will change
the template file for the next fink revision.
Bill
Serge Cohen wrote:
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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 :
>
>> *** For details on how to be removed from this list visit the ***
>> *** CCP4 home page http://www.ccp4.ac.uk ***
>>
>>
>> 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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