rs_fit [id two atoms] or [mol res1 res2]
This command allows one to evaluate how well the molecule fits the density on a per residue basis as desribed by Jones et al. [8]. This implementation differs by outputting the correlation coefficient between the model fragment and the map. This function takes values between -1 and 1. The program generates a residue property [mol]_residue_rsfit that can be used for colouring and selection purposes. The user is free to decide which atoms in each residue contribute to determining the residue fit by loading a suitable table into the database. This table contains an entry for each amino acid type describing what atoms are to be used in the calculation. The following example is part of $ODAT/rsfit_mc.o and would be used if one wanted only main chain atoms in the calculation:
rsfit_PHE T 1 70 N CA C O CB rsfit_PRO T 1 70 N CA C O CB rsfit_SER T 1 70 N CA C O CB
In the $ODAT directory, files also exist for only side chain atoms ( rsfit_sc.o) and all atoms ( rsfit_all.o). The first time through, the program prompts for the map, otherwise the map is defined in RSR_map. The calculation is carried out 5 residues at a time. The following example is edited a bit to reduce output.
O > rs_fit a a1 a20 Util> A A1 A20 C Util> Calculating zone A1 to A20 in molecule A , object C Util> 42 atoms in zone Util> File_RSR_map is not defined. Util> Enter file name [ rsr.map]: ano1.map Util> Map centre: 46.05 55.49 20.79 Util> Grid origin: 29 37 8 Util> Grid extent: 17 17 18 Util> Plus value for this map is: 0 Util> 6 atoms for residue A1 correlation= 0.501 Util> 8 atoms for residue A2 correlation= 0.466 Util> 9 atoms for residue A3 correlation= 0.454 Util> 11 atoms for residue A4 correlation= 0.690 Util> 8 atoms for residue A5 correlation= 0.726 Util> 4 atoms for residue A6 correlation= 0.742 Util> 7 atoms for residue A7 correlation= 0.590 Util> 14 atoms for residue A8 correlation= 0.780 Util> 9 atoms for residue A9 correlation= 0.594 Util> 8 atoms for residue A10 correlation= 0.722 Util> 7 atoms for residue A11 correlation= 0.643 Util> 6 atoms for residue A12 correlation= 0.507 Util> 6 atoms for residue A13 correlation= 0.504 Util> 9 atoms for residue A14 correlation= 0.534 Util> 8 atoms for residue A15 correlation= 0.594 Util> 11 atoms for residue A16 correlation= 0.440 Util> 8 atoms for residue A17 correlation= 0.638 Util> 9 atoms for residue A18 correlation= 0.503 Util> 12 atoms for residue A19 correlation= 0.512 Util> 8 atoms for residue A20 correlation= 0.607 Util> *** garbage collecting *** O > dir a_*rsfit* Heap> A_RESIDUE_RSFIT R W 132
In the calculation of the real space fit of structures to electron density
maps (command Rs_fit) O's default values for the parameters
A(o) and C may not result in correlation coefficients with optimal
discrimination between good and bad electron density fit. Since these
parameters covary, there are multiple ways to obtain the desired result. In
practice, 
can be set to 0.9, and C varied between 0.6 and 1.2 in
steps of 0.05. Selection of the value of C which gives the highest
correlation coeffcient for a residue with good electron density fit should
also give the largest difference between the correlation coefficients of
residues with good and bad density fit. The default value of C = 1.04 has
worked well for maps in the 1.7--1.9Å range, while a value of 0.82 was
better for a map at 2.4Å resolution. In a future version of the
program, it will be possible to refine these values.