Re: [modeller_usage] disulfide bonds in aligned structures?
To: Mike White <>
Subject: Re: [modeller_usage] disulfide bonds in aligned structures?
From: Modeller Caretaker <>
Date: Mon, 24 Sep 2007 11:20:44 -0700
Cc: Modeller_List <>
Mike White wrote:
I have been modeling a homopentamer which should have a disulfide bond
in each subunit in the same position as the multiple templates that we
are using (the alignments have the cys residues of the target lined up
with the disulfide-forming cys in the templates). When I carry out the
alignment of the templates using salign, the XX_fit.pdb files for the
templates do not have the disulfides indicated using SSBOND, even though
the original pdb files (XX.pdb) do have the SSBOND lines in them.
Modeller only reads the ATOM and HETATM records from PDB files - any
other record (including SSBOND) is discarded. (The only exception is if
you turn on salign's write_whole_pdb option, in which case all of the
header information from the original PDB file is preserved - only the
coordinates are transformed - although Modeller does not "understand"
any of that information.)
I know that automodel will automatically include disulfide restraints
if the templates have them. However,the returned models, while
superimposing nicely on the template structure, do not have the
disulfides, even though the cysteines in the model are right where the
disulfide-forming cysteines are in the template. I assume that automodel
uses the XX_fit.pdb files for the fitting routines, and the fact that
the XX_fit.pdb files are missing the SSBOND lines is why the disulfides
are present in the model.
No - automodel does not read (or write) SSBOND records either. It
determines template disulfides using a distance criterion. I'm not sure
what you mean by "uses the XX_fit.pdb files for the fitting routines"
because automodel does not do any kind of template superposition by
default (although you can turn on initial_malign3d).
Alternatively, I guess I could use model.patch as per node24 in the
online manual to force the disulfides to be where I want them to be, but
this just doesn't seem right if the templates all have the disulfide and
the alignments have the cysteines where they should be.
Well, it sounds like automodel has already put in the disulfides for you
("the cysteines in the model are right where the disulfide-forming
cysteines are in the template") so using patch() won't add anything. You
could manually put SSBOND records into your generated models if your PDB
viewer software requires them, but because Modeller does not read them,
you'd be wasting your time trying to introduce them into any of
Modeller's inputs.