You can use the protein visualization software like Chimera to
deselect H-atoms and save rest of the atoms in the protein.
-
Suma
On 4/15/15, Ashutosh Shandilya <izerokelvin.gmail.com> wrote:
> you can use
>
> * sed -i '/^.............H/d'* filename
>
> to delete all the hydrogen from a pdb file.
>
>
>
> On 15 April 2015 at 12:05, muhammad tahir ayub <tahirgp0.gmail.com> wrote:
>
>> Dear All
>> While editing the pdb we need to delete the hydrogens, I
>> have
>> used the following commands but all the hydrogens were not deleted
>>
>> reduce -trim pdbnameH > pdbname
>>
>>
>>
>> *awk '$1=="ATOM" && substr($3,1,1)!="H"' input.pdb > output.pdb*
>>
>>
>> *what can i do for the deletion of all Hydrogen atoms from the pdb
>> filekindly help me in this regard*
>>
>>
>> *Thanks in advance*
>> *Muhammad Tahir*
>> *Ayub*
>>
>> *Junior Research Fellow*
>>
>> *H.E.J Research Institute of Chemistry*
>>
>> *International Centre for chemical and Biological Sciences*
>>
>> *University of Karachi, Pakistan*
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>>
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Received on Wed Apr 15 2015 - 03:30:03 PDT
