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Re: [modeller_usage] gaps in template alignment to query sequence in case of multidomain modelling

On 4/25/10 9:24 PM, saibal das wrote:

i have created a multi domain model using modeller FAQ first method
aligning each template to query sequence and arranging them in PIR
format in multi alignment file. but template is not available for a
large C terminal region of the model. Even template alignment to
query has gap regions between each domains.The model is giving poor
stereochemical properties. is there any solution to this problem.
If there is no template for a part of your sequence, you have only two options with Modeller:
1. Use a more sensitive method (such as profile-profile) to search for templates. 

2. Exclude that part of the sequence from your model.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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