[Jmol-users] Secondary structure does not match DSSP

[Nicholas Newell]

Hello,

I'm using Jmol 14.13, which should use the DSSP v2.0 algorithm to compute 
secondary structure. The command $show defaultStructureDSSP returns true, so 
this
should indeed be the case. However, Jmol displays residues 365-368 from 
7odc.pdb as loop-type, not ribbon, while DSSP 2.0 computes this stretch as type 
E, part of a strand that strectches from residue 365 to residue 373. To 
complicate matters, at residue 369 Jmol does not not start the ribbon at the 
residue's nitrogen but instead at its alpha carbon.

However, if I issue the command $calculate structure and then redisplay, the 
structure is then shown with a ribbon consistent with DSSP, running from 365 to 
373. Can anyone tell me why Jmol doesn't display this stretch according to DSSP 
in the first place? It's true that a ramachandran angle calculation does show 
the stretch 365 to 368 as loop-type with no ribbon, so perhaps for some reason 
Jmol is doing a ramachandran calculation instead of DSSP for these residues, 
but then still doesn't explain why the ribbon starts at residue 369's alpha 
carbon instead of its nitrogen.

It's worth noting that this stretch is somewhat ambiguous in secondary 
structure. Although it shows strand-like H-bonding with an adjacent strand, the 
chain bends tightly enough at these residues to fit the definition of a beta 
turn. Does Jmol override DSSP in such cases?

Any insight is appreciated.

Nicholas Newell--
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Re: [Jmol-users] Jmol 14.14.1 chirality

[Robert Hanson]

argh.  Broke chirality for ketones!

On Fri, Apr 21, 2017 at 11:27 AM, Robert Hanson  wrote:

>
>
> On Fri, Apr 21, 2017 at 11:10 AM, Bruce Tattershall <
> bruce.tattersh...@newcastle.ac.uk> wrote:
>
>> Dear Bob
>>
>>
>>
>> The chirality calculation is clearly useful.
>>
>>
>>
>> I have tried it on my chiral phosphorus compounds, e.g. as in
>>
>> https://www.staff.ncl.ac.uk/bruce.tattershall/structs/bpthiq.php
>>
>> and it finds the chiral carbons in the organic ligands and successfully
>> labels them (as R in this case),
>>
>> but it does not find the chirality of the phosphorus atoms to which they
>> are attached.
>>
>>
> It's a work in progress.
>
> Limitations:
>
>  no parallel chirality paths
>  not processing inositols correctly
>  no lone-pair business
>  standard E/Z, R/S, r/s only; no allenes, no planar asymmetry
>
>
>
>>
>> I have no idea of how this works, but would it be possible to extend it
>> easily to phosphorus chirality (for which
>>
>> one uses the same rules but counts the lone pair as lowest priority)?
>>
>>
> Lone pairs wouldn't be too difficult to add, particularly if they are
> limited to P and S. They are definitely in the IUPAC 2013 spec. I'd like to
> add imine stereochemistry as well.
>
>
>
>>
>>
>> When I first got into measuring NMR spectra of diastereomers of such
>> compounds about 15 years ago,
>>
>> I found it very hard to get my inorganic chemist’s head around the
>> chirality implications.  It would
>>
>> have been very useful to have a tool to work it out for me.
>>
>>
>>
>> If you are going to elements other than carbon, then I guess that besides
>> phosphorus, the inorganic
>>
>> chemist’s favourite, the chirality at silicon, germanium and arsenic
>> could also be useful to people.
>>
>
> Silicon and ammonium are just like carbon, I think. As and P no problem.
>
> Definitely not going to higher valencies any time soon.
>
> Higher priorities are allenes and getting the darned inositol business
> working  correctly. But maybe P and S and As are so easy I should just do
> them
>
> Bob
>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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
--
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