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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 >
