While waiting for knowledgeable help, one possibility is that your pdb
isn't being read flexibly enough (this would be surprising, but would
explain the symptom). In particular, if the 'prime' symbol falls outside
of the column range it is supposed to be in, C5' would read as C5.
You could blindly try shifting the atom name one character to the left
to see if it works:
$ sed 's/ C5'/C5' /g' SAM68-C25-BOX.pdb > newtry.pdb
Bill
On 4/4/17 1:50 AM, Sidhu, Khushwant (Dr.) wrote:
> more SAM68-C25-BOX.pdb|grep -v WAT|grep 5360
> ATOM 5360 C5' C 326 -6.295 26.880 17.879 1.00 0.00
> more SAM68-C25-BOX.pdb|grep -v WAT|grep 5371
> ATOM 5371 C5 C 326 -6.351 30.781 20.616 1.00 0.00
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Received on Tue Apr 04 2017 - 02:30:02 PDT
