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Re: [modeller_usage] Optimization and modelling
- To: Piyush Diyora <yellow_piyu46 AT yahoo.co.in>
- Subject: Re: [modeller_usage] Optimization and modelling
- From: Modeller Caretaker <modeller-care@ucsf.edu>
- Date: Thu, 24 Jun 2010 14:58:53 -0700
- Cc: modeller_usage <modeller_usage@listsrv.ucsf.edu>
On 6/24/10 9:58 AM, Piyush Diyora wrote:
My question is
1) As these fragments are from different protein having different 3d
structure, HOW RELIABLE WILL BE MY PROTEIN 3D STRUCTURE?
You can't tell for sure. Input alignment and sequence identity are poor
indicators of output model quality. This is the job of model assessment.
But when you have multiple templates, you should be particularly careful
in the regions where they overlap, since they may give contradictory
information.
2) If I want to build a model based on the reference template (created
by joining all the fragments), how should i do it? I dont know how to
manually modify the sequence file (which will be used by modeller)
The sequence file is just a plain text file, which you can create in any
text editor.
Ben Webb, Modeller Caretaker
--
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