Fri., Feb. 26th 2010
EBI
Dear all,
I've already replied privately to several people who replied when I first
posted th question, but did not set the record-clear for
the whole community and I do apologize.
What I have is two or more 3D structures, not protein, similar in
their 3D but equivalent atoms don't have the same atom-name. I thought
that in order to rename equivalent atoms automatically I needed to 3D fit
the two structures first. Adel Golovin of PDBeMOTIF fame
(http://www.ebi.ac.uk/pdbe-site/pdbemotif) has pointed out that for the
automatic atom renaming process all I needed was 2D-fitting via 2D-graph
isomorphism routine which he could provide. Once all structures in a given
set have the same atom names, 3D-fitting is doable using numerous
software/utilities.
Thanks again for the replies, especially to Pavel Afonine (phenix)
with whom I had a lengthy exchange.
CCP4-board is one of the best...
Thanks again
Miri
|