Windows users might like to download the free editor Notepad++ ( http://notepad-plus-plus.org/) as a replacement for the dire editor that comes as standard with the OS. This handles end of line conversions, does hex dumps, syntax highlighting etc. You *can* make a decent OS out of Windows - once you obtain enough third party components.
Cheers -- David On 27 September 2011 05:22, Robbie Joosten <[email protected]>wrote: > One would assume that Windows software would read DOS/Windows type text > files... > Open the file in Wordpad. Unlike Notepad, it is able to work with Windows > and Unix type text files. If you edit something and save the file, it will > be in Windows style. If Superpose stops on that, it should really be > updated. I'm sure that there are Windows versions op the programs Unix2dos > and Dos2unix which were the programs to use to convert one type to the > other. You can also use Word to search and replace the linefeeds. > > Good luck with this very retro problem. > Cheers, > Robbie > > > Date: Mon, 26 Sep 2011 17:07:50 -0600 > > From: [email protected] > > Subject: Re: [ccp4bb] Superpose, SSM > > To: [email protected] > > > > > I think something in your workflow is inserting dos line feeds (\n\r or > \r\n, I can't remember which). > > > > If I have guessed correctly, you want to remove those "\r"s before > proceeding (or never let them get in there in the first place). > > > > You claim to open it with MS something, which would insert dos line feeds > as part of Operation Vendor Lock. Did you happen to save it, perhaps by > habit? That would do the trick. It might even do something insidious and > insert those linefeeds without your purposefully saving the document. > > > > Your best bet to fix the file after corruption is vim (used to be that > "crystallographers" could use real text editors). > > > > The command in vim is: > > > > :%s/\r//g > > > > You might find some third party utility that fixes linefeeds for $30.00 > somewhere, if vim is too "retro". > > > > Otherwise, you may want to start over, skip checking it out in MS > something, and go straight to superpose. > > > > James > > > > > > > > On Sep 26, 2011, at 2:51 PM, Matthias Zebisch wrote: > > > > > Hi again, > > > > > > Thanks for your quick replies but I think I made myself not clear. here > is what I'm doing: > > > > > > 1) superpose proteinA.pdb onto proteinB.pdb : works, but gives out > proteinA_lsq1.pdb with extra empty lines (not the anisou lines ;o) ) > > > > > > 2) superpose proteinA_lsq1.pdb onto proteinC.pdb : doesnt work because > proteinA_lsq1.pdb cannot be read > > > > > > Any ideas? > > > Even if there is some compatibility issue between CCP4 and windows, I > guess superpose should be able to read its own files, shouldnt it? > > > > > > Thanks, > > > > > > Matthias > > > > > > > > > On 9/26/2011 9:13 PM, Jacob Keller wrote: > > >> I vaguely recall notepad doing something wacky with files in certain > > >> cases...why don't you get the excellent text editor NoteTab Light > > >> [sic] (I use it all the time--free and works great), then take a look > > >> at your files and see whether MS notepad altered the files. > > >> > > >> JPK > > >> > > >> On Mon, Sep 26, 2011 at 2:42 PM, Matthias Zebisch > > >> <[email protected]> wrote: > > >>> Dear CCP4 users, > > >>> > > >>> I am using the ccp4i version 6.2.0 under windows 7. I've come across > a > > >>> problem with superpose. > > >>> The outputfile appears to have additional line feeds (see picture) > which, > > >>> however are not seen in the windows notepad. > > >>> The structure can also be opened in coot and pymol. However, it is > not > > >>> possible to use it within CCP4, eg. for a subsequent superposition. > > >>> > > >>> Is this problem known to anybody and is there a simple workaround > available? > > >>> I need to compare hell of a lot of relative domain orientations... > > >>> > > >>> I did not have this problem on a second computer with ccp4 6.1.2. > When I > > >>> updated to 6.2.0, the situation was as described above. > > >>> > > >>> Any help will be highly appreciated, > > >>> > > >>> Thanks, Matthias > > >>> > > >> > > >> >
