chiming in from the sidelines: I agree with Bob... The "bug" here is that
PDB structure!
-Tom
On Thu, Feb 10, 2011 at 10:14 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> 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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>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
> ------------------------------------------------------------------------------
> 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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------------------------------------------------------------------------------
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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