[gmx-users] g_helix

[David van der Spoel]

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
>period.
>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.
(phi-phi0)^2+(psi-psi0)^2.
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
>
>
>
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>

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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++