Dear, 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? >Message: 1 >Date: Fri, 03 May 2013 10:31:56 -0700 >From: Modeller Caretaker modeller-care@salilab.org >To: aixintiankong aixintiankong@126.com >Cc: modeller_usage@salilab.org >Subject: Re: [modeller_usage] how to build the loop of protein model > using modeller >Message-ID: 5183F48C.7010601@salilab.org >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >On 4/29/13 8:25 PM, aixintiankong wrote: >> i don't know how to build a model that the protein, NAD+ and ligand >> coexsit and the loop of protein is disordered. > >One way to do this would be to align your model sequence with the first >template (loop is helix) for the entire sequence except the loop, and >the second template (loop is disordered) for the loop: >http://salilab.org/modeller/9.11/FAQ.html#1 > >Another way would be to just use the first template, and just unalign >the loop so Modeller builds it without template information: >http://salilab.org/modeller/9.11/FAQ.html#2 > > Ben Webb, Modeller Caretaker >-- >modeller-care@salilab.org http://www.salilab.org/modeller/ >Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage