How is the helicity calculated ?

Discuss methods to obtain meaningful observables from simulation trajectories. You can share scripts or just ideas and links to other communities are very welcome, too. For Hippo-specific analysis have a look at the Hippo -> Analysis forum.
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m.kalavera
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How is the helicity calculated ?

Post by m.kalavera » Tue Apr 21, 2009 8:07 am

Hello everybody,
my hippo helicity analysis work fine, but I want to understand what is done in the background. Is there a publication or general equation that explains the calculation method ? Actually I don't know how to handle the value "range" in the analysis, because the default state is +-30 degrees, but the Lubert Stryer tells me something about 60 degrees for the perfect dihedral angle in an alpha helix. May be you can help me with this small problem or guide me to some literature.
Thanks allot,
your M.Kalavera

jakob
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Re: How is the helicity calculated ?

Post by jakob » Tue Apr 21, 2009 1:40 pm

Hi,
The standard definition of helicity is used. A residue is considered helical if
phi = -57 deg +- 30 deg
psi = -47 deg +- 30 deg
the 'range' is the 30 deg, and can e.g. be narrowed to +- 20 deg. But 30 is recommended. Remember it is +-, so the arc is 60 deg.
Hope this helps,
Jakob

m.kalavera
Posts: 29
Joined: Mon Feb 09, 2009 10:58 am
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Re: How is the helicity calculated ?

Post by m.kalavera » Wed Apr 22, 2009 9:56 am

Thanks Jakob,
this helped allot. It was my bad, that I have not understood the range value, which is no completely clear.
I just needed to know how you proceed because I want to use the same criterion on my explicit simulations.
Thanks again for your reply,
your M.Kalavera

m.kalavera
Posts: 29
Joined: Mon Feb 09, 2009 10:58 am
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Re: How is the helicity calculated ?

Post by m.kalavera » Tue May 05, 2009 1:51 pm

Hi everybody,
I have a new question again pointing at the helicity. The helicity analysis creates allot of interesting files, as specially the helicity_res.dat. This file contains the helicity in percentage per AA. I assume that this numbers represent the mean value over the whole simulation. Is it possible to extrude this kind of values for some specific frames, e.g the first and the last one or some frames in the middle ? Is there a possibility right at the moment ? Thx for your support !

your M.Kalavera

jakob
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Posts: 6
Joined: Sun Jul 06, 2008 4:54 pm
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Re: How is the helicity calculated ?

Post by jakob » Tue May 12, 2009 6:14 pm

Hi,
Sorry, the helicity analysis is always for the complete simulation, but you can extract the helicity per residue from the helcity_vs_step.dat file, by loading that into e.g. excel and calculating the average of a residue over the time range you need it. The helicity_vs_step.dat file averages every 10 frames into one value, so it will have one tenth the entries than there are frames in the movie.xyz file.
If this is too complicated, there are also other easy secondary structure programs like DSSP that will give you helicity per residue of e.g. a PDB file you provide.
Hope this is helpful,
Jakob

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