Quoting Miguel <[EMAIL PROTECTED]>:
So, in DNA and RNA the sugar forms five-membered rings with the main atoms
C1', C2', C3', C4', O4'.
Note that in some PDB files instead of the prime '
a star * is used (C1*, C2*, C3*, C4*, O4*).
Yes. Jmol supports this.
In fact, I think that all of the .pdb files that I have seen use * ... I
do not recall ever seeing one that used '
If you have one, please send it to me so that I can add it to the Jmol
test files.
The PDB has indeed replaced the prime by an asterisk for naming the
sugar atoms.
Quote from the PDB Format Description
---------------------
* The asterisk (*) is used in place of the prime character (') for
naming atoms
of the sugar group. The prime was avoided historically because of
non-uniformity of its external representation.
---------------------
However, there are still programs that generate PDB files where a prime is
used for naming the sugar atoms. One example is InsightII by Accelrys
(http://www.accelrys.com/products/insight/index.html).
So, Jmol should be able to cope with both versions.
js
Thank you,
Miguel
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