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-<TITLE>pdbShapeFit</TITLE>
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-<H1>pdbShapeFit</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: pdbShapeFit
-Options:
- [-i[nput]pdb[File] InPDB (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-i[nput]mrc[File] InMRC (NULL ).as(inFile ) ] :Essential :InputDataFile
- [-C[ontour] Contour (0.0 ).as(Real ) ] :Essential :Contour
- [-C[ontour]M[ode] ContourMode (0 ).as(Integer ) ] :Optional :ContourMode: refer to mrcImageContourSurfaceCreate
- [-o[utput of ]mrc OutMRC (NULL ).as(outFile ) ] :Optional :OutputDataFile
- [-o[utput of ]txt OutTxt (stdout ).as(outFile ) ] :Optional :OutputDataFile
- [-o[utput of ]pdb OutPDB (NULL ).as(outFile ) ] :Optional :OutputDataFile
- [-xmin xmin (0 ).as(Real ) ] :Optional :xmin for fitting
- [-xmax xmax (0 ).as(Real ) ] :Optional :xmax for fitting
- [-xd[elta] xDelta (1 ).as(Real ) ] :Optional :delta x for fitting
- [-ymin ymin (0 ).as(Real ) ] :Optional :ymin for fitting
- [-ymax ymax (0 ).as(Real ) ] :Optional :ymax for fitting
- [-yd[elta] yDelta (1 ).as(Real ) ] :Optional :delta y for fitting
- [-zmin zmin (0 ).as(Real ) ] :Optional :zmin for fitting
- [-zmax zmax (82 ).as(Real ) ] :Optional :zmax for fitting
- [-zd[elta] zDelta (1 ).as(Real ) ] :Optional :delta z for fitting
- [-E[uler]A[ngle] EulerAngle (ZOYS ).as(String ) ] :Optional :Euler Angle for three-angle
- [-phimin phimin (0 ).as(Real ) ] :Optional :phimin for fitting(degree)
- [-phimax phimax (194 ).as(Real ) ] :Optional :phimax for fitting(degree)
- [-phid[elta] phiDelta (2 ).as(Real ) ] :Optional :delta phi for fitting(degree)
- [-psimin psimin (0 ).as(Real ) ] :Optional :psimin for fitting(degree)
- [-psimax psimax (0 ).as(Real ) ] :Optional :psimax for fitting(degree)
- [-psid[elta] psiDelta (2 ).as(Real ) ] :Optional :delta psi for fitting(degree)
- [-thetamin thetamin (0 ).as(Real ) ] :Optional :thetamin for fitting(degree)
- [-thetamax thetamax (0 ).as(Real ) ] :Optional :thetamax for fitting(degree)
- [-thetad[elta] thetaDelta (2 ).as(Real ) ] :Optional :delta theta for fitting(degree)
- [-P[DB]C[ontour]M[ode]surfaceMode (0 ).as(Integer ) ] :Optional :PDB SurfaceMode: refer to pdbSurface
- [-order order (1.7 ).as(Real ) ] :Optional :order: refer to pdbSurface
- [-refine refine (2 ).as(Integer ) ] :Optional :refine: refer to pdbSurface
- [-size size (3 ).as(Integer ) ] :Optional :size: refer to pdbSurface
- [-weight weight (100 ).as(Real ) ] :Optional :weight: refer to pdbSurface
- [-mergin mergin (3.0 ).as(Real ) ] :Optional :mergin: refer to pdbSurface
- [-thres thresHold (0.0 ).as(Real ) ] :Optional :threshold: refer to pdbSurface
- [-I[nverse] ] :Optional :Black is High Density.
- [-Centre ] :Optional :Filament-axis is x=0, y=0
- [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
- [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
------ Additional Usage -----
- -ipdb : Filename : An atomic model to be fitted (PDB)
- -imrc : Filename : 3-D density map (mrc-formated)
- -omrc : Filename : fitting score map (MRC)
- z=0: a max-score map of an phi-z plane which includes a max score point.
- The max score mean a maximum score in all x-y-psi-theta plane with specific values of phi and z.
- z=1: a max-score map of an psi-theta plane which includes a max score point.
- The max score mean a maximum score in all x-y plane with specific values of psi, theta, phi and z.
- z=2: a score map of an x-y plane which includes a max score point.
- -otxt : Filename : fitting results (Text)
- -opdb : Filename : An atomic model with a maximum score after fitting
- -x|y|zmin : Initial value of z (should <= zmax)
- -x|y|zmax : Final value of z
- -x|y|zd : Delta z for fitting (should !=0)
- -phi|psi|thetamin : Initial value of phi (should <= phimax; initial value of phi is 0)
- -phi|psi|thetamax : Final value of phi (should !=0)
- -phi|psi|thetad : Delta phi for fitting (should >0)
- -C : Contour level of map file
- -Inverse: Protein has high density on the image
- -Centre : Filament-axis in an inPDBFile is along the line of x=0, y=0
- -EA : Euler Angle Set : ZOYS: z -> y -> x
- -c : Not used now
- -m 0 : Count the atom number inside the contour.
-</PRE>
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+/bin/bash: pdbShapeFit: そのようなファイルやディレクトリはありません
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+/bin/bash: pdbShapeFit: No such file or directory
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