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.
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.
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.
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.