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To explain the quoting .... >From 6.0.2, ccp4i indeed adds quotes around filenames (for all programs). This is part of the solution of the long-standing problem on Windows where files couldn't be in ...\Documents and Settings\... for example (note the spaces). Hopefully, you no longer need to be so careful where you put your files. Also in CCP4 6.0.2, the phaser parser was updated to handle the quotes and the version changed to 1.3.3 Earlier versions of Phaser indeed read the quotes literally. So this case sounds like a new GUI wrapping an older phaser?? The quoting of XYZOUT_ONOFF is a mistake, since it's not a filename. It may well be that the phaser parser can't cope with that, I'll check. Regards Martyn -----Original Message----- From: [EMAIL PROTECTED] on behalf of William Scott Sent: Fri 12/15/2006 10:36 PM To: Chris Richardson; [email protected] Subject: Re: [ccp4bb]: Re: Phaser problems in Mac OS X 6.0.2-2 *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** 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: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > 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 >>> >> > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.3 (Darwin) > > iD8DBQFFgyFO5EPeG5y7WPsRAntbAJwKQ25fvxNh/rHzyc0LAd9XJ1PqQgCeIqIY > k5fNBuDd5NCEZ7H6MxG0Mx4= > =Z6TN > -----END PGP SIGNATURE----- >
