[gmx-users] about using do_dssp for a few residues

[Xu, Jianqing]

Sounds good!

Thank you Justin!

Kind regards,

Jianqing



-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: 18 November 2013 21:51
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] about using do_dssp for a few residues



On 11/18/13 4:08 PM, jianqing wrote:
> Will appreciate if anyone could provide any suggestions!
>

The only secondary structure that should be affected would be beta-sheets, since their hydrogen bonding patterns are based on non-local interactions.  Helices, bends, and turns should show up independently of any other residues.

Your initial conclusion was correct - do_dssp, like any other program, only considers atoms within the index file provided.

If you only care to visualize those residues of interest, manually modify the .xpm file.  You can make sensible figures by providing an .m2p file on the original .xpm so that it renders better.  The default representation is usually unintelligible, but proper manipulation of the x- and y-axis ratio can yield a very nice figure.

-Justin

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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