Re: protonate

From: David A. Case <>
Date: Tue, 8 Apr 2003 09:06:21 -0700

On Tue, Apr 08, 2003, S.Swaminathan wrote:
> i see that the 3rd column (atom name) is shifted
> slightly to the left, when compared to the original
> pdb file. Why is it so ? Can we avoid it ?

Try the "-b" option.

> What happens to the last two columns of the input pdb?
> (they are absent in the protonated output file).

Protonate discards the sequence numbers (if this is what you mean by the
"last two columns"); they would be out of order anyway if new atoms were
to be added. You will have to change the code if you need these.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Tue Apr 08 2003 - 17:53:01 PDT
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