Category: S.030 - rs_fit
Just follow the recipe below:
- 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 !)
- tell O which map to use with RSR_MAP
- 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:
- find one residue which fits very well and one which fits
very poorly (by eye or using the default values)
- A0 can usually be kept constant at ~0.9
- 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)
- 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
- mail your results to "gerard@xray.bmc.uu.se" for
inclusion in the table above