Years ago Jmol did not have a way of adapting to bizarre structures as well
as it does today, and the PDB database was littered with bizarre structures.
It's not a bug; Jmol requires an alpha carbon, not a nitrogen to define a
protein.
If you can find a number of additional structures in the PDB database that
are similar, we can look into it. Otherwise, it's just not worth adapting
Jmol to show this one structure, and allowing "protein" to include groups
not having an alpha carbon would be very difficult to manage (and probably
introduce all sorts of bugs and also slow down ALL rendering). I suggest,
since you know the structure, just add "or THR" to your "protein" selection
Bob
On Thu, Feb 10, 2011 at 10:56 AM, Eric Martz <ema...@microbio.umass.edu>wrote:
> Dear Bob,
>
> Each of the 4 chains in 1hjx ends with a residue, Thr383, for which
> only a single atom, the main chain nitrogen, has coordinates. Jmol
> (including 12.0.31) fails to recognize this atom as protein, despite
> it being within group THR.
>
> restrict not (protein, nucleic, hetero)
>
> should always select zero atoms, since every atom must be a member of
> one of those three groups. In the case of 1hjx, it selects 4 atoms,
> the nitrogens of THR383 in each of the 4 chains.
>
> I believe this is a bug. Years ago, there were many such bugs in
> Jmol. FirstGlance checks for such "anomalous atoms" and marks them
> with a "?", and spacefills them along with "ligand". I haven't seen
> any anomalous atoms for a long time, but noticed this one recently.
>
> Thanks, -Eric
>
>
>
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The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
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