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Re: [modeller_usage] Quick Question on Automodel



Hello all,

Any additional comments or suggestions on this issue?
So far I have not been able to make modeller follow my alignment.

Is there an explicit way to tell modeller which residue (in the template) must be aligned with which residue in the sequence?

ie:
align->template:1:21 to sequence:7:27

I'm looking to keep the structure identical in some segments.. and have modeller make a best guess in other parts.

Best
Pedro

El lun, 1 mar 2021 a las 20:01, Pedro Guillem (<">>) escribió:
Thank you Ben.

Effectively. T should be 7 but it is being numbered as 4. Even with dashes indicating 6 gaps before the T.

Sorry if I wasn't clear. By offset I ment the output positions not following my alignment.

Yup. the "..." in the sequence is just the rest of the sequence (to make the message shorter) :)

Best
Pedro


On 2/28/21 1:00 PM, Pedro Guillem wrote:
> I'm trying to model from a known template (ident 37%).
> The template is missing the first 3 residues in the structure.
>
> - I start reading the template at position 4.
> - I add 3 dashes to the beginning of the template to compensate for the
> missing residues. (otherwise I get a "residue mismatch" error from modeller)

Dashes/gaps do not have any effect on which residues are read from the
PDB file; this is controlled entirely by the PIR header (the line
starting with "structureX", where you - apparently correctly - have 4 as
the start residue number). Dashes/gaps only control the correspondence
between target and template residues.

> Here is a bit of my ali file. I want the TRL of the template to align
> with the TRM of the sequence.

Your alignment looks fine to me, assuming by "..." you mean "the rest of
the sequence goes here". (A literal "." has a special meaning to
Modeller; read in the manual about modeling with ligands.)

> When it finishes, the position of TRM has a different offset in relation
> to TRL

Not sure what you mean here, unless you were expecting T to be numbered
4. Modeller numbers residues in your model starting from 1, regardless
of your alignment. If you want a different numbering, use
rename_segments(); see
https://salilab.org/modeller/10.0/manual/node23.html
and
https://salilab.org/modeller/10.0/manual/node30.html

        Ben Webb, Modeller Caretaker
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