What I usually do for this is make a copy of the PDB file and change all
the atom x-y-z positions to "1.000". Then I use something like
reforigin or my "origins.com" script to shift the original coordinates
via allowed symmetry operations, origin shifts, or perhaps indexing
ambiguities until it is as close as possible to the "reference", which
is at 1,1,1. I use 1,1,1 instead of 0,0,0 because there are generally
at least two symmetry-equivalent places that are equidistant from the
origin. Declaring the reference to be a bit off-center breaks that
ambiguity, and also biases the result toward having all-positive x,y,z
values.
In case it is interesting, my script is here:
http://bl831.als.lbl.gov/~jamesh/scripts/origins.com
You need to have the CCP4 suite set up for it to work. Run it with no
arguments to get instructions.
-James Holton
MAD Scientist
On 12/13/2017 5:50 AM, Kajander, Tommi A wrote:
Hello,
If someone could point this out would be very helpful... Wasnt there a
simple script somewhere that would transfer coordinates close to
origin - if they for some reason are not? Just cant find anything
right away. Sure i have done this before...
Thanks,
Tommi
