This menu is a collection of analysis programs that generate database blocks that should be of some interest to the user. Values generated in these datablocks can be used for colouring, for selection purposes, or plotted with the Graph pull-down.
Pep_flip - determines if peptide directions are unusual
RSC_fit - determines how well residues match the most similar rotamer
RS_fit - detemines how well residues match the electron density
YASSPA - determines the secondary structure of each residue
pep_flip <id two atoms> or <mol res1 res2>
This command allows the user to locate peptide conformations that are unusual. The technique has been described by Jones et al (1991) and will not be repeated here. If the database of structures has not been loaded, then it will be loaded before carrying out the calculation. It must, therefore, be properly defined in Lego_setup . The command makes a residue property called <mol>_residue_pepflip
Example:
O > pep_flip a a1 a20
Util> Calculating zone A1 to A20 in molecule A , object C
Util> The DB is now being loaded.
Util> Loading data for protein:HCAC
Util> Loading data for protein:PA
Util> Loading data for protein:51C_3
Util> Loading data for protein:ACT_2
Util> Loading data for protein:APP_2
Util> Loading data for protein:AZA_1
Util> Loading data for protein:B5C_2
Util> Loading data for protein:BP2_1
Util> Loading data for protein:C2C_3
Util> Loading data for protein:CPA_5
Util> Loading data for protein:CPV_1
Util> Loading data for protein:CRN_1
Util> Loading data for protein:CYT_4
Util> Loading data for protein:DFR_3
Util> Loading data for protein:ECD_1
Util> Loading data for protein:FB4_1
Util> Loading data for protein:FDX_1
Util> Loading data for protein:FXN_3
Util> Loading data for protein:HIP_1
Util> Loading data for protein:INS_1
Util> Loading data for protein:LH1_1
Util> Loading data for protein:MBO_1
Util> Loading data for protein:NXB_1
Util> Loading data for protein:OVO_1
Util> Loading data for protein:PCY_1
Util> Loading data for protein:PPT_1
Util> Loading data for protein:PTI_4
Util> Loading data for protein:PTN_2
Util> Loading data for protein:REI_1
Util> Loading data for protein:RHD_1
Util> Loading data for protein:SGA_2
Util> Loading data for protein:SN3_1
Util> Loading data for protein:SNS_2
Util> Loading data for protein:TLN_3
Util> Residue A3 has a pep_flip r.m.s. value of 1.43
Util> Residue A4 has a pep_flip r.m.s. value of 0.41
Util> Residue A5 has a pep_flip r.m.s. value of 2.54
Util> Residue A6 has a pep_flip r.m.s. value of 1.56
Util> Residue A7 has a pep_flip r.m.s. value of 0.54
Util> Residue A8 has a pep_flip r.m.s. value of 0.69
Util> Residue A9 has a pep_flip r.m.s. value of 0.40
Util> Residue A10 has a pep_flip r.m.s. value of 0.70
Util> Residue A11 has a pep_flip r.m.s. value of 0.83
Util> Residue A12 has a pep_flip r.m.s. value of 0.50
Util> Residue A13 has a pep_flip r.m.s. value of 0.96
Util> Residue A14 has a pep_flip r.m.s. value of 0.97
Util> Residue A15 has a pep_flip r.m.s. value of 1.96
Util> Residue A16 has a pep_flip r.m.s. value of 1.53
Util> Residue A17 has a pep_flip r.m.s. value of 0.67
Util> Residue A18 has a pep_flip r.m.s. value of 0.33
Util> Residue A19 has a pep_flip r.m.s. value of 0.81
Util> Residue A20 has a pep_flip r.m.s. value of 0.23
O > dir a_*pep*
Heap> A_RESIDUE_PEPFLIP R W 132
O >
rsc_fit <id 2 atoms> or <mol res1 res2>
This option compares the users side chain coordinates with the rotamer library. It finds which rotamer is most like the user's conformation and evaluates the r.m.s. deviation of the side chain atoms after superimposing the main chain atoms. These values are stored in a datablock <mol>_residue_rsc .The location of the side chain rotamer database must have been defined with the lego_setup command.
The following side chains are treated specially:
PHE & TYR's Chi2's are changed by 180° to force the the equivalence of CD1&2 and CE1&2
ASP's Chi2 and GLU's Chi3 are changed by 180° to force equivalence of carboxylate oxygens.
In the calculation of the real space fit of structures to electron density maps, the parameters Ao 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, Ao 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 1.7-1.9 Å range, while a value of 0.82 was better for a map at 2.4 Å resolution. In a future version of the program, it will ne possible to refine these values.
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 (1991). This implementation differs by outputing 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 $ODAT/rsfit_mc.o and would be used if one wanted only main chain atoms in the calculation
rsfit_PHE T 1 70
N CA C O CB
rsfit_PRO T 1 70
N CA C O CB
rsfit_SER T 1 70
N CA C O CB
Files also exist for only side chain atoms ($ODAT/rsfit_sc.o) and all atoms ($ODAT/rsfit._all.o).
The first time through, the program prompts for the map, otherwise the map is defined in RSR_map Only 'mappage'd/brix maps can be used. 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]:
/usr/people/alwyn/o/example/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 Ao 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, Ao 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 1.7-1.9 Å range, while a value of 0.82 was better for a map at 2.4 Å resolution.
yasspa <molecule> <template> <cut-off distance>
An option to define the secondary structure of a protein, given a set of Ca coordinates.
The template molecule MUST reside in the users database. It is normally supplied in the $ODAT/ directory as an O type file. Current templates are alpha.o and beta.o corresponding to a-helices and b-strands. These coordinates are the central members of a cluster analysis (Jones, unpublished) using a 0.5Å cutoff (the default value to YASSPA). To define a-helices use this 0.5Å cut-off. For b-strands use 0.8Å (this is because b-strands show more deviation from the central cluster). If it does not exist, The option creates a residue property <molecule>_residue_2ry_struc. The following example colours a molecule depending on secondary structure:
mol a
yasspa a alpha 0.5
yasspa a beta 0.8
pain_prop res_2ry = ' ' yellow
pain_prop res_2ry = alpha red
pain_prop res_2ry = beta green
ca ; end