[MMTK] all atom pdb to c alpha

Naomi Fox fox at cs.umass.edu
Sun Jun 10 17:17:07 UTC 2012


Not sure what the commands in MMTK are, but if you don't care about losing
the header at the top, you are only working with single-model files, and
just want the ATOM lines, you can just use grep.

For example:
grep ^ATOM 1HHP.pdb | grep ' CA ' > 1HHP_just_CA.pdb

Then to apply to many files, you can call grep in a bash for-loop.
So if all your pdb files are in the same directory, you can do:

for f in *.pdb;
 do grep ^ATOM $f | grep ' CA ' > `basename $f .pdb`_just_CA.pdb
done

On Sun, Jun 10, 2012 at 10:08 AM, Tasneem Ali <tasneem.ali2011 at gmail.com>wrote:

> hello,
> Is there any way software to convert all atom PDB files into the files
> containing only C-alpha atoms. I have to convert around 13000 files, so ,i
> need some smarter way.
>
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