Hi Rick, to follow up on dcor with correl, I have another question:
I am using the dcor function without any problems but wondering whether my setup is appropriate. Currently, I copy my .crd to a comparison set using "coor copy comp"
then use the lines below to calculate dcor between two protein domains.
My question is: is the "orient mass sele" with respect to one (in this case, transmembrane) domain meaningful, or should I be using the entire protein? Should I orient with "mass" or without, and should I be using all backbone atoms? I guess these are physics questions, but maybe you can help. Thank you.
correl maxt 5000 maxa 1000 maxs 6
enter a atom XYZ sele @domain1 end
enter b atom XYZ sele @domain2 end
! reorient each frame with respect to Transmembrane domain
traj firstu 32 nunit 1 orient mass sele tmd end
dcor a b