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 int
I presume you have a dictionary for both SAM and SAH? You need SAM at
least to use COOT.
My method is to calculate a difference map with the SAM density - xclude
all atoms like SAH or waters which might overlap SAM, then manually grad
the SAM to the right place and run real space refinement
Yuan Cheng wrote:
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.
2)Coot: I tried to superpose SAM to SAH in coot. Bot SSM superpose and
LSQ superpose didn't work. when I did SSM supe
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 ring
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
S
