Re: [modeller_usage] determination of symmetry

[Modeller Caretaker <modeller-care@ucsf.edu>]

rathankar rao wrote:
> Iam in to modelling assignment of a zinc finger protein, which has 
> nearly 6 zinc fingers
> The nearest template (1MEY) to it covers only 50% of the sequence length 
> and has 3 fingers corresponding to 3 chains in the template. 
> 1. i would like to know the method of representing the alignment in .ali 
> file for chain breaks

Use the / character to represent a chain break in your alignment. See 
http://salilab.org/modeller/manual/node175.html

> 2. i modelled this in a different manner. I aligned the query with the 
> template for only 50% of the sequence and assumed that these chains 
> belong to different pdb files and hence modelled the query protein like 
> what we do for a chimeric protein(without DNA chains).
> *Outcome: *i got a 3D Model which did not represent the actual template, 
> since the coordinates of DNA was not incorporated in it. I dont know why 
> DNA was not built and as a result, the protein appeared to be bent.

To model DNA is like modeling any other non-standard ligand; see 
http://salilab.org/modeller/FAQ.html#10

	Ben Webb, Modeller Caretaker
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