Thanks Phil,

did this:

egrep -v '^ATOM|HETATM.*H$' m.pdb > m_noH.pdb

Result:

in input file (m.pdb) I have:

ATOM      1 N   GLY A   1       0.504 -0.494   0.924 1.00 7.85
ATOM      2 CA GLY A   1       1.272   0.589   0.277 1.00 6.79
ATOM      3 C   GLY A   1       1.700   1.614   1.301 1.00 5.59
ATOM      4 O   GLY A   1       1.434   1.460   2.496 1.00 6.04
ATOM      0 H1 GLY A   1       0.452 -1.280   0.308 1.00 7.85
ATOM      0 H2 GLY A   1       0.959 -0.765   1.772 1.00 7.85
ATOM      0 H3 GLY A   1      -0.420 -0.171   1.131 1.00 7.85
ATOM      0 HA2 GLY A   1       2.157   0.171 -0.225 1.00 6.79
ATOM      0 HA3 GLY A   1       0.659   1.070 -0.499 1.00 6.79
END

Output file (m_noH.pdb) contains only:

END

Pavel

On 2/6/14, 12:03 PM, Phil Jeffrey wrote:

Of course, because in the shells that I use it will attempt to do variable name substitution in strings that are double-quoted. (I make no warranties about all possible shells). However if you use single quotes:

egrep -v '^ATOM|HETATM.*H$' your.pdb > your_noH.pdb

Should work just fine in tcsh, csh at the very least.

Phil

On 2/6/14 2:52 PM, Pavel Afonine wrote:

Hi Tim,

On 2/6/14, 10:52 AM, Tim Gruene wrote:

the simple and qucik command

egrep -v "^ATOM|HETATM.*H$" your.pdb > your_noH.pdb

should also work.

just out of curiosity I did (copy-paste of your example)

egrep -v "^ATOM|HETATM.*H$\" m.pdb > m_noH.pdb

and I got:

Illegal variable name.

Pavel

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