Hi everyone,
I am trying to model a S-adenosylmethionine (SAM) molecule into the
active site of a protein using the SAH (exists in the crystal structure)
as the template.
What I have already tried but failed so far are
1)Pymol: I loaded the pdbs of SAM and protein-SAH into pymol and copy
SAH into a separate object. Then I tried to align SAM to SAH, but it
didn't work and pymol said " Executivealign:Mobile selection must derive
from one object only". Does anyone know what this mean?
2)Coot: I tried to superpose SAM to SAH in coot. Bot SSM superpose and
LSQ superpose didn't work. when I did SSM superpose, coot said "can't
make graph for SAH structure". when I did LSQ superpose, nothing
happened after I run it. I also tried Extensions> modeling> superpose
ligands, nothing happened too. Does anyone know what's wrong here?
I know that I can probably manually move SAM to the position of SAH and
change the bond angles to make SAM align to SAH. I am wondering if there
is any program that can help to perform ligand alignment without the
need for manual adjustment.
Thank you very much for your suggestion!
Yuan
