[Chimera-users] Problem with Large Molecules

[Thomas Goddard]

Hi,

  The problem opening the biological unit PDB file for virus capsids
1aym and 1p5y is that you are running out of memory.  The asymmetric
unit is small

  1aym (human rhinovirus 16) 7000 atoms
  1p5y (canine parvovirus) 4400 atoms

but with the 60-fold icosahedral symmetry, these become 420,000 atoms
and 264,000 atoms.  Chimera requires about 2-3 kbytes per atom, so you
will need a computer with at least 1 Gb and preferably 2 Gb of physical
memory to open these.  With less memory the machine will become extremely
slow as it uses your hard-disk to cache data that won't fit in the physical
memory.

  I opened the 1aym biological unit on a Mac desktop machine which has
1.5 Gbytes of physical memory in a few minutes.  Chimera was using about
1 Gbyte after it opened.

  To open the model with less memory you could make a new PDB file
containing only the CA backbone atoms, or just CA, C, N, and O
backbone atoms.  That would require writing a script to filter out the
other lines of the file.  We could give you the backbone only files if
you want.

  Another approach is to just open the asymmetric unit and use the
Chimera multiscale tool (Tools / Multiscale / Multiscale Models) to
make the 60 copies.  This does not copy all the atoms so it does not
need alot of memory.  You open the asymmetric unit and press the
"Make models" button at the bottom of the Multiscale dialog to display
the full capsid.  Here are images of 1aym and 1p5y I just made this way:

	http://www.cgl.ucsf.edu/home/goddard/temp/1aym.png
	http://www.cgl.ucsf.edu/home/goddard/temp/1p5y.png

You can also show some of the capsomeres as ribbons or all atom displays.
But if you use Multiscale and try to show the full capsid at atomic or ribbon
level, then it will try to copy the asymmetric unit 60 times and you will
again need alot of memory.

  More images of virus capsids using the Multiscale tool are on our web
site

	http://www.cgl.ucsf.edu/Research/virus/

and on the VIPER web site

	http://viperdb.scripps.edu/


    Tom