VMD-L Mailing List

From: Yi Shang (mirandaisbest_at_gmail.com)
Date: Wed Sep 09 2009 - 13:31:17 CDT

Dear all,
I have a quick question about "measure fit" command.
I learned from the mailinglist that this command could be used for
superimposing two molecules. So I tried it on two PDB structures. From Tcl
output it seems it's calculating the matrix. But two molecules just stayed
where there were -- the command is not moving molecules in the display
window. So I wonder if it's because I need extra plugin/conditions to use
this command.
Below is the command I typed in Tcl, and I am using VMD 1.8.6. In VMD main
window, both molecules are displayed, activated, and not fixed.
===========================================================================
>Main< (VMD) 2 % set sel [atomselect 1 "serial 560 579 598 611 622 629 639
2498 2517 2536 2549 2560 2567 2577"]
atomselect0
>Main< (VMD) 3 % set ref [atomselect 2 "serial 368 387 406 419 433 440 450
1907 1926 1945 1957 1971 1978 1988"]
atomselect1
>Main< (VMD) 4 % measure fit $sel $ref
{-0.309560984373 -0.537274956703 0.784542918205 38.356502533} {0.94680505991
-0.0978629440069 0.306566536427 -13.4308233261} {-0.0879328325391
0.837710261345 0.538989186287 -17.8832244873} {0.0 0.0 0.0 1.0}
=============================================================================
Thank you all! 

-- 
Miranda