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Re: [modeller_usage] RE : help with residues numbering

BESSADOK Anis wrote:
> I'm a new user of modeller, I want to know how to conserve residue
> numbering between my target sequence and the MODEL?

By default, Modeller numbers the output model sequentially starting from
1. It does not use the residue numbering from the template. There is a
good reason for this - how would you number residues that are not
aligned with your template? For example, in the second line of your
sequence you have the primary sequence 'NRSDINDT---GFFMN' which is
aligned with gaps in your template. So what would the residue numbers be?

Secondly, you cannot define residue numbering for a sequence in your
alignment file:

>> P1;1pgp
> sequence:1pgp:43: :630:::::

The various fields in the alignment header instruct Modeller how to read
structural information from a PDB file. They don't make any sense (and
are ignored) for a sequence that has no structure. So you may as well
say "sequence:::::::::" here. The 1pgp, 43, and 60 fields are not used.
A sequence does not have residue numbers - they are a property of the

If all you want to do is have your final model be numbered sequentially
starting at residue number 43, that is straightforward. There is a
rename_segments() command that will do that - see
http://salilab.org/modeller/9v6/manual/node177.html for an example. You
can either postprocess your models with this command, or add it into
automodel.special_patches() or automodel.user_after_single_model() to do
it automatically for each generated model.

If you really want to take residue numbering from a template, there is a
res_num_from() command that will do that. But remember that regions in
your model that are not aligned with a template will not be renumbered.

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage