[gmx-users] re:surface normal direction

Markus O Kaukonen mokaukon at cc.helsinki.fi
Thu Mar 4 14:22:00 CET 2004

>>Dear All,
>>Is ther a tool in the gromacs package to define the
>>surface normal direction of a membrane protein based
>>on orientation of alpha helices.

>how about g_bundle?

Since this may be of general interest could you
describe how to get the vector pointing to +z direction
with g_bundle and perhaps after that rotate protein
so that z axis points to 001 direction.

I managed to get nice rasmol picture of the membrane protein with
axis on it, but could not work out the explicit z direction from the
output files of g_bundle.

Sorry for this stupid question, but could not quite follow the the
documentation of g_bundle...

Best Wishes, Markus

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