2 RMS_FIT
Keyword: RMS fit, superposition, rotate, translate
File: rms_fit.txt
Last modified: 18-nov-97

The RMS_FIT items superimpose two molecules using a RMS fit
procedure.  They rotate and translate the "from" segments
"to" the target segments.

The RMS_FIT menu block is loaded with the file
"MAIN_CMDS:load_rms_fit.com".  If you want more than provided
then copy the macro "MAIN_UTILS:rms_fit_1_to_2.com" to your
working directory and modify it.  


3 FIT_PAIR

If molecules are far from being superimposed and you can not
use the "FIT_SEQU" item, because sequence id's are not
related as well provide your pair list manually.  Go to page 1
and click INIT_PAR to initialize the pair list and then
after picking each pair off atoms you want to superimpose
click MAKE_PAR.  The direction is "from - to", don't mess
this up utherwise the superposition will not be what you
expect.  

After you are done, click the FIT_PAIR item, which will
perform the superposition according to the provided pair
list.

3 FIT_DIST

It is assumed that molecules are more or less superimposed
already.  So the pair list is generated using a distance
criterion [default cutoff is 1.5A] trying to superimpose
selected atoms [default atom name is CA] of two provided
segment names.  List of segment names and wild signs are
accepted.

3 FIT_SEQU

When you know that sequence ids of two molecule match
use this option.  sequence ids will be used
to create a pair list, which will be then used in the
fitting procedure.

After the first fitting step the second fit based on a pair
list created on a distance criterion always follows.