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Bug #209

"Ellipticity at 222 nm" provided by g_helix

Added by tiboli empty about 11 years ago. Updated about 11 years ago.

Status:
Closed
Priority:
Normal
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

g_helix reports the number of helical residues instead of ellipticity at 222 nm in the cd222.xvg file.

David recommended the following suggestion in the email list.

Check the routine ellipticity in src/tools/hxprops.c
Right now what is plotted is the number of helical residues. There is
also a magic number w in the data. If you have the Hirst and Brooks (JMB 1994 243 173-178)
paper handy I'm sure you can fix the routine. Please send me back the
corrected code.

History

#1 Updated by David van der Spoel about 11 years ago

On line 96 of hxprops.c you can try to replace
ell+=Xi;
by
ell+=ppw[j].w;

There is no way to verify this of course...

#2 Updated by David van der Spoel about 11 years ago

I dug up the old paper and the implementation is now according to their Eqn. 1 using the 13 bin table. This will be present in the next release.

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