Yuan Cheng wrote:
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
Dear all,
Thank you very much for your suggestions! It turned out that I
didn't give the correct residue number (I should use 1) when I did "LSQ"
and "superpose ligands". The above two methods gave very similar overlay
results. After one round of real space refinement, SAH and SAM fit with
each perfectly. I have not tried other suggestions yet. I bet they will
probably work too! Thanks again!
Yuan
