[gmx-users] g_helix

David van der Spoel spoel at xray.bmc.uu.se
Sat May 25 11:57:52 CEST 2002

On Sat, 25 May 2002, Richard Filmer wrote:

>The analysis program 'g_helix' outputs a file, helicity.xvg (not mentioned
>in manual), that gives average helicity/residue over a specified time
>On what basis does it determine whether or not a residue is helical? it
>seems to be far more conservative in its assignment than DSSP.
>Thank you,
It computes the MSD from the phi/psi angles.
If that's less than 64 degrees^2 it is a helix. That maybe too
conservative. You can change it on line 85 in src/tools/hxprops.c

>Richard Filmer
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Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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