Hi Paul,

from my perspective just replacing spaces with dashes or underscores prior to populating the file select dialog would do the trick. If Windows users insist on spaces in filenames for they OS this could be done in an OS dependent fashion, I suppose.

Your assumption of merging the ligand is correct for standard crystallographic procedures, were one deals with one defined ligand in the receptor. We are using coot for fragment based screening. That means we are dealing with a cocktail of ligands we have to consider for each dataset. Sometimes the nature of the ligand cannot be identified from the density alone, so we are real space fitting all/most of them and merging only one of them for future refinement and writing out the others so we have them handy in case the refinement did not pan out. Hence the need for writing out the ligands separately.

But regardless of how our procedures are, I think spaces in filenames under Unix in general are not such a good idea. Better to avoid these potential pitfalls in the first place, IMHO.

Cheers

	Carsten


> -----Original Message-----
> From: Mailing list for users of COOT Crystallographic Software
> [mailto:[log in to unmask]]On Behalf Of Paul Emsley
> Sent: Thursday, August 23, 2007 10:02 AM
> To: [log in to unmask]
> Subject: Re: [COOT] Question/comment about filenames containing spaces
> 
> 
> Schubert, Carsten [PRDUS] wrote:
> >
> > I was wondering if the file naming conventions could be 
> changed in a 
> > way to be more Unix friendly/compatible.
> >
> Hmm...
> 
> > A user here was playing around with the ligand fitting tools. Turns 
> > out that the fitted ligands are named something like "Fitted Ligand 
> > #1". Upon saving through the file selector box, the default name is 
> > something like "Fitted Ligand #1-coot-0.pdb"
> >
> Indeed.
> 
> > The spaces in the file name pose all kinds of problems 
> later on. Linux 
> > per se does not seem to mind, but some applications just 
> wont cooperate.
> >
> Broken "other applications", I'd say.  With my trusty tab 
> key, I don't 
> have problems with file names with spaces.
> What other applications? (Don't tell me ccp4i, that would be 
> a Bad Thing!)
> 
> > I guess it is not a problem for the casual user to change 
> the name in 
> > the file select dialog, but having to do this on a day to day basis 
> > becomes a tad tedious.
> >
> Hmm... yes... But typically (or so I thought) one would want to Merge 
> Molecules on (correct) fitted ligands and discard the rest - 
> and so the 
> issue of fitted ligand file names would not arise.
> 
> Also, anything tedious should be scripted and bound to a key or a 
> trivial gui.  Tell us to what file name you would change 
> "Fitted Ligand 
> #0-coot-0.pdb" "Fitted Ligand #1-coot-0.pdb" etc and I will 
> write you an 
> extension to Just Do It.
> 
> Having said that, Steven Sheriff (IIRC) has already asked for some 
> flexibility in default file names.  I've been thinking about 
> that for a 
> bit and maybe there is a solution that will fit both.
> 
> Paul.
>