[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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>
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