AMBER Archive (2002)

Subject: pdb file

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Fri Nov 22 2002 - 18:41:01 CST

Hi Amber users,

I hope that someone can help me with this, I am not sure what is causing
me the problem.

I have a pdb file with a protein channel. In its own system of coordinates
the channel is not align on the OZ axis and I want to reorient the channel
with the axis channel to be parallel to OZ.
What I did is I plot the original coordinates in matlab and it seems that
the channel is parallel with the bisector of the (XOZ) plane so then I
apply the coordinate transformation
xnew(i)=(x_init(i)-z_init(i))/sqrt(2);
znew(i)=(x_init(i)+z_init(i))/sqrt(2);
If I replot the new coordinates in matlab the protein is indeed reoriented
and parallel to OZ.
Then I make a new pdb file with the new coordinates and load the pdb
file in leap. However in xleap my structure is completely gone.

Does anyone have an idea what could cause this? I would appreciate your
help

Thanks,
Ioana

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