[phenixbb] how to remove hydrogen from pdb
Pavel Afonine
pafonine at lbl.gov
Thu Feb 6 12:33:09 PST 2014
Hi Phil,
ok, now I tried this:
egrep -v '^ATOM|HETATM.*H$' m.pdb > m_noH.pdb
Input (m.pdb - file right from PDB):
ATOM 1 N GLY A 1 0.504 -0.494 0.924 1.00
7.85 N
ATOM 2 CA GLY A 1 1.272 0.589 0.277 1.00
6.79 C
ATOM 3 C GLY A 1 1.700 1.614 1.301 1.00
5.59 C
ATOM 4 O GLY A 1 1.434 1.460 2.496 1.00
6.04 O
ATOM 0 H1 GLY A 1 0.408 -1.171 0.354 1.00
7.85 H
ATOM 0 H2 GLY A 1 0.939 -0.775 1.648 1.00
7.85 H
ATOM 0 H3 GLY A 1 -0.298 -0.189 1.160 1.00
7.85 H
ATOM 0 HA2 GLY A 1 2.052 0.220 -0.166 1.00
6.79 H
ATOM 0 HA3 GLY A 1 0.731 1.013 -0.407 1.00
6.79 H
END
Output (m_noH.pdb):
END
Just to be clear: none of the two commands suggested so far worked on a
valid PDB file (above). So I thought it might be useful to point this out.
All the best,
Pavel
On 2/6/14, 12:21 PM, Phil Jeffrey wrote:
> So I guess your contribution at this point in the thread is just to be
> as difficult as possible ? I dare say if you use it on PROTIN format
> it won't work either.
>
> Try it on a file that actually puts out something that conforms to the
> PDB standard with the element line at the end, not something that
> almost conforms to the standard, has non-distinct index numbers,
> apparently missing spaces on the GLY:N atom.
>
> I would hope, modulo the usual list of bugs, that phenix.refine
> actually writes out something more closely resembling the correct
> format, in which case Tim's regular expression would actually work.
>
> From the original post:
> >> Actually i refine my structure with phenix along all hydrogen now
>
> Phil Jeffrey
> Princeton
>
> On 2/6/14 3:09 PM, Pavel Afonine wrote:
>> Thanks Phil,
>>
>> did this:
>>
>> egrep -v '^ATOM|HETATM.*H$' 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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