3 <TITLE>pdbRhoFitTm</TITLE>
11 [-i[nput]pdb[File] InPdb (NULL )] :Essential :InputDataFile
12 [-i[nput]mrc[File] InMrc (NULL )] :Essential :InputDataFile
13 [-o[utput of ]mrc OutMrc (NULL )] :Essential :OutputDataFile
14 [-Sx Sx (50 )] :Essential :x of rotation axis
15 [-Sy Sy (110 )] :Essential :y of rotation axis
16 [-Sz Sz (110 )] :Essential :z of rotation axis
17 [-o[utput of ]txt OutTxt (NULL )] :Optional :OutputDataFile
18 [-o[utput of ]pdb OutPDB (NULL )] :Optional :OutputDataFile
19 [-xmin xmin (0 )] :Optional :xmin for fitting
20 [-xmax xmax (0 )] :Optional :xmax for fitting
21 [-xd[elta] xDelta (1 )] :Optional :delta x for fitting
22 [-ymin ymin (0 )] :Optional :ymin for fitting
23 [-ymax ymax (0 )] :Optional :ymax for fitting
24 [-yd[elta] yDelta (1 )] :Optional :delta y for fitting
25 [-zmin zmin (0 )] :Optional :zmin for fitting
26 [-zmax zmax (82 )] :Optional :zmax for fitting
27 [-zd[elta] zDelta (1 )] :Optional :delta z for fitting
28 [-E[uler]A[ngle] EulerAngle (ZOYS )] :Optional :Euler Angle for three-angle
29 [-phimin phimin (0 )] :Optional :phimin for fitting(degree)
30 [-phimax phimax (194 )] :Optional :phimax for fitting(degree)
31 [-phid[elta] phiDelta (2 )] :Optional :delta phi for fitting(degree)
32 [-psimin psimin (0 )] :Optional :psimin for fitting(degree)
33 [-psimax psimax (0 )] :Optional :psimax for fitting(degree)
34 [-psid[elta] psiDelta (2 )] :Optional :delta psi for fitting(degree)
35 [-thetamin thetamin (0 )] :Optional :thetamin for fitting(degree)
36 [-thetamax thetamax (0 )] :Optional :thetamax for fitting(degree)
37 [-thetad[elta] thetaDelta (2 )] :Optional :delta theta for fitting(degree)
38 [-n[ormalize]w[eight]normalizeWeight (100000000.0)] :Optional :weight for normalize
39 [-n[ormalize]C[ontour]normalizeContour (0.0 )] :Optional :Contour Level for Normalize
40 [-I[nverse] ] :Optional :Black is High Density.
41 [-Zminus ] :Optional :Shift to -z
42 [-Tfactor ] :Optional :Consider T factor
43 [-T[ factor ]lim[it] Tlim (60 )] :Optional :The atom will be neglected
44 [-Centre ] :Optional :Filament-axis is x=0, y=0
45 [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
46 [-m[ode] mode (0 )] :Optional :Mode
47 [-C[ontour] contourLevel (0.0 )... ] :Variable :ContourLevel
51 -ipdb : Filename of pdb file of atomic model
52 -imrc : Filename of mrc file of contour map
53 -omrc : Filename of mrc file of fitting results
54 -otxt : Filename of text file of fitting results
55 -opdb : Filename of pdb file with a max score after fitting results
56 -zmin : Initial value of z (should <= zmax)
57 -zmax : Final value of z
58 -zd : Delta z for fitting (should >0)
59 -phimin : Initial value of phi (should <= phimax; initial value of phi is 0)
60 -phimax : Final value of phi (should >0)
61 -phid : Delta phi for fitting (should >0)
62 -C : Contour level (variable and MUST be last option)
63 -Inverse: Protein has high density on the image
64 -Sx : x of rotation axis
65 -Sy : y of rotation axis
66 -Sz : z of rotation axis
67 -Zminus : Atomic model shift to -z while fitting
68 -Tfactor: Consider temperature factor
69 -Tlim : The atoms whose T factor is above Tlim will be neglected
70 -Centre : Filament-axis is x=0, y=0
72 -m 0 : Count the atom number inside the contour.
73 1 : Add the densities of atoms.