[phenixbb] how to remove hydrogen from pdb

[Phil Jeffrey]

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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