We currently have a repository of viral capsid structures at
http://viperdb.scripps.edu
We also dealt with this issue a while ago. We also found it "problematic" to
show the
whole biological unit, full capsid (because of the likely high number of
atoms for some entries
and the possible memory limitations on the clients). We concluded that it is
not necessary
to do so for spherical capsids and that it suffices if only the neighboring
units to the central
icosahedral asymmetric unit, CIAU (on the VIPERdb convention), are shown, in
order to appreciate
the interfaces and interactions generated upon capsid assembly.
At first we tried to use the biomat info (translation+rotation matrices)
from the PDB as you have
suggested. Then we realized there was an alternative for the case of
spherical capsids; we
know the cage vertices (vectors) the biounit is 'inscribed' into (VIPERdb
convention), and the
angles that relates all the copies around these vertices. Therefore, we can
use a 'rotateSelected'
command to create all the needed 'duplicates' (we got a lot of help from Bob
on this ;)
An excerpt from the code to manage one of the 5-fold symmetry related
copies, for example, follows:
set echo top center;echo Calculating|Duplicates;refresh;
select :*.Ca/2.1;
n_models = getProperty("modelInfo","modelCount");
ini = n_models + 1;
fin = n_models + 4;
x = data("selected", "pdb");
subu_count = 0;
for (var i = ini; i <= fin; i = i + 1)
subu_count = subu_count + 1;
DATA "append @x";
m = "*/"+i+".1";
select @m;
ang = 72.0 * subu_count;
rotateSelected MOLECULAR AXISANGLE {0.0,87.9,142.2} @ang;
trace 0.5;
end for
set drawHover TRUE;
draw five_fold_01 "5-fold Axis" ARROW 110 DIAMETER 1 {0.0,0.0,0.0}
{0.0,87.9,142.2};
frame all;display displayed;refresh;select none;set echo off;
A couple of 'live' examples of this can be found here:
a T=1 virus
http://viperdb.scripps.edu/info_page_big_jmol.php?VDB=1a34
or a T=3 virus
http://viperdb.scripps.edu/info_page_big_jmol.php?VDB=2bbv
Please note that the user interface and the options provided are still in
development, but still you can get a good idea
of how it works.
This is just an alternative and I am aware this tactic can not be used in
all general cases, or at least
no as straight forward, but perhaps it can help someone else in the mean
time the biomat info can be of use.
--
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://www.scripps.edu/~trippm
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