This is great Bob, and is exactly what I was after last month (,
my apologies if I was not clear enough then ;)
Now, as for an spherical capsids 'user' at VIPERdb, I would like to be able to:

1) have the option to show/hide any of the biomolecules in the PDB file, in spherical capsids there's always 60. This doesn't mean all 60 biomolecules should be loaded initially by default, but only when the user chooses to. The default will always be to load and show biomolecule number one. As I understand it, every time the user wants to display another biomolecule in the biounit, the PDB file needs to be (down)loaded again and read using a different filter? If so, I think it would be more practical (but perhaps more trouble to implement) to load the PDB file once, save all the biomats corresponding to all the biomolecules in the biounit, and then use them latter as needed? (this might save a lot of HTTP requests ;) I'm thinking about buttons to show 1/4, 1/2 or full capsid. But also an option to show biomols 1,6 and 7 (or any combination), to present an specific interface.

2) have the option to apply symmetry to any number of chains in the ASU (many capsids have more than one chain in the ASU), I believe one can do that with the filter as is, right? I'm thinking of the option to show chain A of biomol 1 and chain C of biomol 7 (or any combination), again, to present an specific interface.

3) have the option to apply symmetry just to a segment of an specific chain in the ASU, I believe one can do that with the filter as is, right? I'm thinking about the option to show only the residues involved in an specific quaternary structure, beta annulus for example, around an icosahedral symmetry axis, comprised from a few residues of chain B of biomol 1, a few from chain C of biomol 6, and so on ...

I'm thinking on implementing an ad hoc UI for the above, so I don't know about the Jmol menu. Although I guess for other systems it would be nice to have a list of all biomols available.

4) have all the biomolecules (as whole or parts, as explained above) as different model/frame to apply different representations to them. So, "load append" works?

Some, or all, of the points above might be valid for other systems too. As you said Bob, this is huge, and I'm very exited about it, will certainly simplify the scripts we use, and more importantly, the way people interact with these structures and learn from them.

Thanks again for the great work!

Date: Tue, 29 Apr 2008 09:34:25 -0500
From: Bob Hanson <>
Subject: [Jmol-users] Jmol load FILTER "SELECT *.CA; BIOMOLECULE n;
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

biomolecule oriented Jmol users:

OK, I'm convinced by my colleagues here at St. Olaf and Carleton that
this is HUGE. Just playing with it a bit, I'm totally excited. You can
now load a subset of the atoms in a PDB file into Jmol (a limited SELECT
sort of filter to the LOAD command that works at the file-reading level
for PDB files) and then also select one of the BIOMOLECULE
specifications in the "REMARK 350" biological unit section of the header
and apply the symmetry described in that header.

Thank you to Eric, Rolf, and Dan for suggesting this. I believe that the
next version of Jmol you see, 11.5.32, will have this working correctly.
I've done a navigation mode fly-through of the entire 60-unit simian
virus (1sva.pdb) looking at helices and sheets as I flew, and I'm sold.
On my 1.2Gb-memory laptop Jmol rotates 124,000 atoms with cartoons like
nothing in real time. So I think we are onto something.

Now, interface. What do you want? I presume a menu entry under the main
"symmetry" entry should be the place to start. What options do you need?

 -- option to replace or append?
 -- option to apply symmetry?
 -- list of biomolecules available (with # of atoms involved if symmetry
is applied?)

anything else on that menu?

I suspect as people play with this more, they will want me to expand on
that load filter select option. What else?


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
/ |
0 |

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