Please keep this on the mailing list.
What you have sent me is an old style PDB file. Better go and download the file in the latest PDB format. If you inspect your file you will notice hydrogen labels like "1HH1" which your awk substring search obviously can't match and hence you will still have those particular hydrogens in output.pdb. Recent PDB formats have changed this and you would find this label to be "HH11". Apparently reduce can't handle this either. But since this is a properly formatted PDB file and thus has the element names in columns 77-78 properly designed software should be able to handle this...
BTW, I have noticed that some of the records in your PDB are partially shifted to the left. You have to make sure to properly align those entries as it is likely that software can't handle this. The PDB format is a fixed column format.
________________________________________
From: muhammad tahir ayub [tahirgp0.gmail.com]
Sent: 16 April 2015 19:09
To: Loeffler, Hannes (STFC,DL,SC)
Subject: deletion of H atoms for pdb file
Dear Cheers,
I have attached the following original and edited pdb file i have obtained after applying the
awk '$1=="ATOM" && substr($3,1,1)!="H"' input.pdb > output.pdb
the reduce command just deleted all the data of pdb file
1cgh.pdb = original pdb file
1cgh_ed.pdb = pdb file after application of awk command
Muhammad Tahir Ayub
Junior Research Fellow
H.E.J Research Institute of Chemistry
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Received on Thu Apr 16 2015 - 12:30:04 PDT
