From: Rolf Huehne <rhuehne@fli-leibniz.de>

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 <hansonr@stolaf.edu>

> 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
/ | trippm@scripps.edu
0 | http://viperdb.scripps.edu/