VMD-L Mailing List

From: Kuen Phon Wu (kpwu_at_tel.life.nthu.edu.tw)
Date: Wed Mar 07 2001 - 22:50:24 CST

Dear VMD-L:

I have 10 DNA molecules with similar 3D struture.

I try to source the rmsd.tcl from VMD 1.6 to align and get the
rmsd value. When I use the align window to align the 10 DNA,
what name I can choose?

Using "name C5" or "name P" to align all DNAs is working now,the rmsd
value is smaller than the value from InsighII caculation. Also ,if I enable
the backone check box,error message exists.

Is there any command I can align the backbone of DNA without the two
flexible end.

Thanks for any help.

Kuenphon Wu.