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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