From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Mar 30 2012 - 01:25:16 CDT
Of course it looks messy because the pdb format has a fixed column format.
That means vmd is searching for the coordinates at a special range within a
line in the pdb file, because sometimes there are also no spaces between the
values so they need to be identified by their positions. So having residue
names bigger than 4 characters will brake the pdb columns and there is no
[easy] way to read such a file properly. So what would help, in the simplest
way IMHO to just replace the residue names before generating the pdb or
afterwards. The easier would be afterwards by a little bash script for
example. The tool sed can replace strings in files very fast and easy "sed
-i ‘s/original_word/new_word/g’ file.txt" and the file is changed in place.
If you are able to, you can also write the script in a way, that in can
parse a description file like
#Long #Short <- don't write this to the file
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