Re: [modeller_usage] modeller_usage Digest, Vol 12, Issue 17

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

On 5/8/13 12:37 AM, aixintiankong wrote:
> thanks for you help. should i use the  the entire second template(loop is
> disordered) sequence or only  part of the disordered sequence to aglian?

You would definitely need to exclude the ligand and any part of the 
sequence that interacts with the loop (otherwise Modeller will have a 
hard time positioning the ligand, since it will get conflicting 
information). But you can include the rest of the protein if you want - 
since you said the sequences are very similar I doubt it would make much 
difference either way.

	Ben Webb, Modeller Caretaker
--
modeller-care@ucsf.edu             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage