VMD-L Mailing List

From: Leontyev Igor (ileontyev_at_ucdavis.edu)
Date: Tue Feb 03 2009 - 15:51:02 CST

I used VMD tool for matching structures without any problem until tried to
fit atom triplets. For these structures the command "measure fit" in a
script produces irrelevant transformation matrix. Program move second
structure far away (to almost infinity) instead of aligning the structures.
Use of graphical RMSD Tool leads to the same result. The structures are
given bellow. I use VMD with WindowsXP. How the problem can be fixed?

seltriplet0.pdb:

CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 C18 HEA X 516 41.696 310.454 201.293 1.00 0.00
ATOM 2 C19 HEA X 516 40.504 310.822 201.821 1.00 0.00
ATOM 3 C27 HEA X 516 40.284 312.095 202.581 1.00 0.00
END

seltriplet1.pdb

CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 C18 HEA X 515 47.812 311.246 202.665 1.00 0.00
ATOM 2 C19 HEA X 515 47.564 312.299 203.472 1.00 0.00
ATOM 3 C27 HEA X 515 46.342 313.148 203.243 1.00 0.00
END