[phenixbb] how to remove hydrogen from pdb
Pavel Afonine
pafonine at lbl.gov
Thu Feb 6 12:09:55 PST 2014
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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