[phenixbb] how to remove hydrogen from pdb

[Phil Jeffrey]

So I guess your contribution at this point in the thread is just to be 
as difficult as possible ?  I dare say if you use it on PROTIN format it 
won't work either.

Try it on a file that actually puts out something that conforms to the 
PDB standard with the element line at the end, not something that almost 
conforms to the standard, has non-distinct index numbers, apparently 
missing spaces on the GLY:N atom.

I would hope, modulo the usual list of bugs, that phenix.refine actually 
writes out something more closely resembling the correct format, in 
which case Tim's regular expression would actually work.

 From the original post:
 >>  Actually i refine my structure with phenix along all hydrogen now

Phil Jeffrey
Princeton

On 2/6/14 3:09 PM, Pavel Afonine wrote:
> 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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>
>
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