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
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