Dear BB Readers, I have used CCP4 on Windows exclusively for nearly 10 years now. The text editor of choice for PDB files coming out of CCP4 has always been WORDPAD, which comes with Windows, no need to download. NOTEPAD causes me great difficulty with PDB files, probably because of my age, but let's not get hung up on that. I have never been interested enough in chasing up ways of using NOTEPAD properly.
In the last couple of months, CCP4 started outputting PDB files that appeared in WORDPAD as one continuous line, i.e. no line feed. This was an INTERMITTENT behaviour. I could not reproduce it to order. These files are readable by NOTEPAD, despite my dislike of this editor. I have not changed anything in my set up or in the CCP4 or Coot installation. So I could blame it on some system updates in WINDOWS that are invisible to me, but then again it could be a fault of something else, perhaps like changing the <CR><LF> combination already mentioned. The files are usually readable in COOT, which reads anything coming out of CCP4, but again output from COOT is occasionally unreadable in CCP4. NOTEPAD readable files are usually OK. Unfortunately, I don't have a recipe for correct action. Having said all that, at the moment output PDB files from CCP4 and COOT appear to be all well behaved in terms of readability, both in the Windows editors and in CCP4. I would like to think this problem has disappeared just as it had appeared suddenly. I shall continue to look out for symptoms of trouble. Pierre ******************************************************* Dr Pierre Rizkallah, Senior Lecturer in Structural Biology, Wales Heart Research Institute, Heath Campus, Cardiff CF14 4XN email: [email protected] phone + 44 29 2074 2248 -----CCP4 bulletin board <[email protected]> wrote: ----- To: [email protected] From: Robbie Joosten Sent by: CCP4 bulletin board Date: 27-09-2011 05:22 Subject: Re: [ccp4bb] Superpose, SSM 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 > >>> > >> > >>
