I am a new MODELLER user. I am trying to duplicate a result in
literature using v8.1 of MODELLER, and am trying to use 1H8C.pdb as
template to model 1D3Z.pdb structure. I followed the basic outline of
the scripts in the tutorial (and attached the scripts I used). At the
end of modelling, the homology model I obtain is about 9A cRMSD from
the target structure, whereas in the literature an earlier version of
MODELLER (v6.2) was used to achieve a closer structure to the template
(1.9A cRMSD). I was wondering whether there is any simple step I may
be missing.
Are you using the same sequence alignment as the authors of the
published work? If the homology is not high there might be some
subjective decisions made in the alignment regarding the position of
loops/insertions that could significantly affect those parts of the
structure. If they didn't publish their alignment you might want to
write to them and ask for it.
Also, you might want to try comparing RMS values that exclude regions
where the backbone of the template is disordered, since Modeller might
generate significantly different conformations for those regions
depending on the random number seeds.
--
Eric Bennett, Center for Drug Design, U of Minnesota
I am not a vegetarian because I love animals. I am a
vegetarian because I hate plants. - A. Whitney Brown