Hi Sean,
if you want to do mapping by alignment, all PyMOL alignment commands
support an "object" argument which creates an alignment object.
See the example on this PyMOLWiki page:
http://pymolwiki.org/index.php/Get_raw_alignment
Note that for cealign the support for the object argument got a
Hi Krisztina,
if the order of atoms is identical in both molecules, mapping is
possible. The easiest way is to make a copy of the reference molecule
and update its coordinates from the other molecule.
create mol3, mol1
update mol3, mol2, matchmaker=0
delete mol2
See also: http://pymolwiki.org/
I too have encountered a similar problem and was hoping that somebody had a
suggestion for this. I've tried using CEALIGN to attempt to align the
molecules and then hoped that I could simply use some atom-atom pairwise
distances to map one set of atoms onto another but CEALIGN doesn't seem to
Hi,
I have two chemically identical molecules, but with different residue names,
residue numbers and atom numbers. However the atom coordinates are also
different. Is there some script that could map down the atom names, residue
names and numbers to each other?
Thanks for any ideas!
Krisztina
