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*To*: ccp4bb@dl.ac.uk*Subject*: [ccp4bb]: displaying ATOM vectors with NPO*From*: "Gregory D. Bowman" <gdbowman@phoenix.Princeton.EDU>*Date*: Mon, 7 Feb 2000 18:03:01 -0500 (EST)*Sender*: owner-ccp4bb@dl.ac.uk

*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html *** Hello, I am having difficulty with NPO and plotting atoms onto Harker sections. I have some possible patterson peaks which I have traced back to real x y x fractional coords (in theory). When I make patterson vectors with VECTORS, and read it into NPO, the logfile (and .ps files) indicate that no atoms were picked for the X=1/2 and Y=1/2 Harkers, but atoms were picked (as I would expect them to be) for the Z=0 Harker. Of course ANY atoms I feed to VECTORS should give peaks at X=1/2, Y=1/2 and Z=0 for this spacegroup (P4212). Indeed, the VECTOR output lists patterson peaks which, when converted to fractional coords indicate X=1/2 and Y=1/2, but these are not being read in by NPO for some reason. Is there some CARD I am missing or something? Any suggestions are most welcome! Greg ================================ Here are the scripts I am using: vectors xyzout ./siteE <<+ symmetry 90 psymm 123 cell 35.52 35.52 60.98 90.00 90.00 90.00 xyzlim 0.0 0.5 0.0 0.5 0.0 0.5 ATOM E 0.08 0.20 0.14 + #================================ npo \ MAPIN Pt1_14b2_patt_1X.map \ XYZIN ./siteE.brk \ PLOT Pt1_14b2_patt1X_atom.plot \ << END-npo TITLE 15.0 - 3.5 ISO Patt X Harker # Contour map MAP SCALE 3 CONTRS SIG 0.5 1.0 1.5 2.0 2.5 SECTNS 0.5 0.5 1 grid 0.05 0.05 # Coordinate input INPUT BROOK RESIDUE RED SELECT ALL LABEL ALL JOIN RADII RESIDUE V 0.01 SOLID NOHID # Plot out PLOT END-npo #============================================= npo \ MAPIN Pt1_14b2_patt_1Z.map \ XYZIN ./siteE.brk \ PLOT Pt1_14b2_patt1Z_atom.plot \ << END-npo TITLE 15.0 - 3.5 ISO Patt Z Harker Sig=0.2-0.8 # Contour map MAP SCALE 3 CONTRS SIG 0.2 0.4 0.6 0.8 SECTNS 0.0 0.0 1 grid 0.05 0.05 # Coordinate input INPUT BROOK RESIDUE RED SELECT ALL LABEL ALL JOIN RADII RESIDUE V 0.01 SOLID NOHID # Plot out PLOT END-npo #============================================== Some output for the pattX (from NPO): ..... Boundary for input coordinates and for cell edge -0.0014 0.5014 0.4267 0.1046 -0.0008 0.5008 0 atoms written to scratch file 10 Data Line---- JOIN RADII RESIDUE V 0.01 12 bonds found Data Line---- SOLID NOHID Data Line---- PLOT Drawing_Size = 327.0000 Picture_Scale = 3.0000 Perspective_Distance = 600.0000 ***Begin Plotting*** No atoms in sections 16 16 -------------------------------------- Some output for the pattZ (from NPO): Boundary for input coordinates and for cell edge -0.0014 0.5014 -0.0014 0.5014 -0.0425 0.0425 16 atoms written to scratch file 10 Data Line---- JOIN RADII RESIDUE V 0.01 12 bonds found Data Line---- SOLID NOHID Data Line---- PLOT Drawing_Size = 327.0000 Picture_Scale = 3.0000 Charcter_Size = 2.0000 Perspective_Distance = 600.0000 ***Begin Plotting*** 24 atoms selected in sections 0 to 0 16 of these atoms included in plotting 36 bonds found . . .

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