RE: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio)

From: Ross Walker <>
Date: Wed, 14 Jun 2006 13:06:49 -0700

For the record - at least on RedHat EL4 there appears to be a mac2unix
command. Although I have never tried it (I just found it in fact)... Your
suggestion to use a 'better' editor is definately the way to go.
All the best

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From: [] On Behalf Of
Knut Langsetmo
Sent: Wednesday, June 14, 2006 12:56
Subject: Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di

the problem is in the original use of "textedit". the standard end of line
character in a mac is the carriage return character (which will show up
on the unix side as ^M), while in unix uses a line feed (dos/win uses
a carriage return-line feed pair). so the suggestion to use the command
dos2unix will not work in this case. there are many ways to deal with it.
the simple command "tr '\r' '\n' < macfile.txt > unixfile.txt" should work.
alternatively, you can use vi, and change from <cr>(mac) to <lf> (unix):
:set fileformat=unix

or to change back the other way:
:set fileformat=mac

it also works for windoz land:
:set fileformat=dos

and to tell the difference:
set statusline=%<%f%h%m%r%=%{&ff}\ %l,%c%V\ %P

but my favorite is to use a different text editor in the first place. some
alternatives for the mac running osx are alphax (my favorite, mostly because

it was my first), and subethaedit (probably currently the best)


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Received on Sun Jun 18 2006 - 06:07:10 PDT
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