Hi Dan,
Thank you so much! Changing the anchored molecule fixed the problem!
Hailin Huang
On Wed, Aug 7, 2013 at 12:11 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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 - 13:00:04 PDT
