Miri,
For matching similar small molecules you can try in CCP4mg as
described at
http://www.ysbl.york.ac.uk/~ccp4mg/ccp4mg_help/superpose.html#interactive_selection
the 'user defined' superposition option with 'monomer' mode. This
does 2D graph isomorphism for the atoms in one residue.
Liz
On 26 Feb 2010, at 16:57, Miri Hirshberg wrote:
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
