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Re: [modeller_usage] [salign] concerning the manual : feature 2 and structure superposition
- To: Benjamin SCHWARZ <schwarz.ben AT gmail.com>
- Subject: Re: [modeller_usage] [salign] concerning the manual : feature 2 and structure superposition
- From: Modeller Caretaker <modeller-care@ucsf.edu>
- Date: Mon, 24 Oct 2011 10:25:23 -0700
- Cc: modeller <modeller_usage@listsrv.ucsf.edu>
On 10/24/11 7:18 AM, Benjamin SCHWARZ wrote:
Reading the salign documentation
(http://salilab.org/modeller/manual/node300.html) I have troubles
understanding a specific paragraph concerning feature 2.
Given that you don't say what you think it might mean, all I can do is
restate it and hope it makes more sense. ;) To calculate feature 2, the
Euclidean distance between residues in two structures, the structures
must be aligned. So SALIGN does this, but that alignment is only a
temporary one; it is used only to determine the values of feature 2. The
final alignment is done in the regular way, by dynamic programming using
*all* features.
Ben Webb, Modeller Caretaker
--
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