From: Rolf Huehne <[EMAIL PROTECTED]>
>
> We must be careful not to mix up terms here. As far as I understood the
> "biomolecule" is always a whole biologically active unit.
>
> In the case of Mauricio's virus capsid there is only a single
> biomolecule and it consists of the asymmetric unit plus 59 copies
> generated by symmetry operations.
>
>
I might have been using terms in a bad way then. I've been thinking
of the whole capsid as a biounit, which is the one biologically active, and
each copy of the ASU as biomolecules, which by themselves have no biological
activity. Now I see both (biounit, biomolecule) are interchangeable (
http://pdbwiki.org/index.php/Biological_unit).
Thanks for the correction.
>
> As far as Bob has described the filter options yet, I don't think that
> it is currently possible to apply only a subset of the symmetry
> operations of a specific biomolecule. So with the virus capsid you would
> always get 60 copies of whatever you selected by the filter (e.g. only 1
> chain out of 3) into a single model/frame. And if you wanted to display
> only only one half of the capsid you could use for example the following
> command:
>
> display symop<=30
>
> How this half would really look like would of course depend on the order
> of the symmetry operations (e.g.: a ball might look afterwards like a
> ball with holes and not like one half of a ball).
Good point. Although we take care in producing the transformation matrices
always
in the same order and sequentially when processing the original PDB file (we
discard
all biomat info, re-orient the ASU to a standard location and generate all
the new 60
biomats -in the VIPERdb standard orientation these are the same for all
capsids actually-)
So I think 'display symop<=30' should work.
>
>
> Regards,
> Rolf
>
>
> From: Bob Hanson <[EMAIL PROTECTED]>
>
> > OK, so for example, if I want to display 1/2 capsid, I will have to load
> > the PDB file 30 times, each time using a different select in the
> > loading filter.
>
> heavens, no. You just load it once, then display only the parts of the
> capsid you want (if you can settle for just *.CA atoms). If you want all
> the atoms, I think you probably can't load 1/2 the capsid anyway.
>
I see. That's what we're using for the duplicates method in our current
implementation (*.CA atoms)
>
> > In addition to the intra-unit interfaces (protein-protein interactions
> > between the chains that form the
> > ASU), one is also interested in seeing/studying the inter-unit
> > interfaces (protein-protein interactions
> > between the chains of different copies of the ASU). Some of these
> > inter-unit interfaces are formed by
> > up to six copies of the ASU, all sharing a common symmetry axis (in
> > this case, a 6-fold symmetry axis).
> >
>
> Right, so probably what we want to add to the filter is the capability
> of selecting specific BIOMT records.
>
That would be great. How complex the selection on the filter can be? Could I
select, for example,
residues 5-20 from chain A and res 41-50 from chain B, and then apply BIOMT
1,6 and 7?
>
> >
> > In most cases there is no need to generate a full capsid (it looks
> > pretty awesome
> > though ;). Because of symmetry, ~1/4 capsid contains all interfaces of
> > interest.
>
> Still a lot of atoms if you want all of them.
Right. For that kind of display only CA will have to do. But when we have a
few
residues per chain (see above) that need to be transformed/copied, all atoms
shouldn't be a problem.
--
0 | Mauricio Carrillo Tripp, PhD
/ | Department of Molecular Biology, TPC6
0 | The Scripps Research Institute
\ | 10550 North Torrey Pines Road
0 | La Jolla, California 92037
/ | [EMAIL PROTECTED]
0 | http://viperdb.scripps.edu/ <http://www.scripps.edu/%7Etrippm>
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