Hi Yuan,
LSQ within Coot works quite well for superimposing similar ligands. Are you sure you are selecting the appropriate chain IDs and residue numbers in the LSQ dialog box? It is a rigid body superposition though so it will only get you in the neighborhood (i.e. the adenine and sugar rings should at least superimpose well and then you may have to manually adjust the rest). If you have electron density for the SAH, the 2 ligands are similar enough that you could then use real space refinement to get the SAM to superimpose almost perfectly on SAH. You would have to read a restraint file for SAM (which can be obtained by uploading the SAM coordinates into the PRODRG server) into coot for this though.
Good luck,
Eric
PS - SSM will not work for ligands, as you saw.
__________________________
Eric Larson, PhD
MSGPP Consortium
Department of Biochemistry
Box 357742
University of Washington
Seattle, WA 98195
On Wed, 3 Mar 2010, 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
>
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