Hi,
I received your files and was able to take a look at your system.
First, for the size of the system (8 protein molecules; 2x5557 atoms,
2x3103, 2x896, and 2x 289 atoms plus 2 ADP residues and various ions)
the box size is (in my opinion) somewhat small (106x143x109 Ang),
which makes imaging tricky.
On Mon, Aug 5, 2013 at 1:41 PM, Hailin Huang <hailin.huang.my.liu.edu> wrote:
> protein was not auto-imaged but just flipped 180 degrees. (I was trying to
The protein is not actually flipped at all. You can verify this
visually by looking at the two frames side-by-side; the first molecule
(residues 1-337, which is what autoimage uses as the 'anchor' molecule
by default) is translated to the center of the box. The second
molecule (which is 'fixed' to the anchor) is imaged (again just a
translation) appropriately so that it is close to the anchor, and so
on and so forth. The 8th protein molecule (residues 1158 to 1214) is
not imaged even though it seems it belongs next to the 7th protein
molecule (residues 963-1157) because that would move it farther from
the 'anchor' molecule. Basically, autoimage is working as advertised,
but the autoimage command's guess at the first molecule being a good
'anchor' is not ideal.
However, if I choose the somewhat smaller but less compact third
protein molecule (residues 356-550) as the 'anchor', the imaging
results look good to me. You may need to play around with your
'anchor' to get the best results. In general the best choice for an
'anchor' is the molecule which covers the most volume in your system.
Hope this helps,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Aug 07 2013 - 09:30:02 PDT
