Q.030 - How do I get the most out of RS_FIT ?

Category: S.030 - rs_fit

Just follow the recipe below:

  1. calculate a map covering the molecule(s) for which you want to calculate RS-fit values and mappage it (e.g., using MAPMAN; make sure to conserve the entire dynamic range of density values in your mappaged map !)
  2. tell O which map to use with RSR_MAP
  3. execute the command: rs_fit mol residue1 residue2 object

  You may need to optimise the parameters A0 and C (use RSR_SETUP
to do this).

  Some reported values (more contributions are welcome !):

 Resolution (A):	A0:	C:	Remarks:
 ===============	=====	=====	========
 ~ 0.9 - 1.2		?	?	(come on Keith/Zbyszek)
 1.38			1.05	0.92	Miri Hirshberg
 ~ 1.5 - 1.6		?	?
 ~ 1.7 - 1.9		0.90	1.04	(defaults)
 ~ 2.0 - 2.3		0.90	0.91	Christina Divne
 ~ 2.2			0.90	0.90	Christine Gaboriaud
 ~ 2.4			0.90	0.82	Sherry Mowbray
 ~ 2.6 - 2.8		?	?
 ~ 2.9 - 3.0		0.85	0.95	Gerard Kleywegt
 ~ 3.2 - 3.5		0.85	0.55	Gerard Kleywegt
 ~ 3.5 - 4		0.85	0.75	Gerard Kleywegt (3.8 A)
 less than 4		?	?	?

If you want/need to optimise these values, proceed as follows:

  1. find one residue which fits very well and one which fits very poorly (by eye or using the default values)
  2. A0 can usually be kept constant at ~0.9
  3. vary the value of C between 0.5 and 1.2 in steps of 0.05 and do rs-fit for the zones around the good and the bad residue (include two residues at both sides, e.g. if a69 is your good residue, do rs_fit mol a67 a71)
  4. the best value for C is that which gives the largest difference between RS-fit(good) and RS-fit(bad); ideally, RS-fit(good) will also be maximal at this value of C and RS-fit(bad) will be minimal
  5. mail your results to "gerard@xray.bmc.uu.se" for inclusion in the table above