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