README.dotpackconts Home Page: Richardsons' Laboratory Dec 1998


You will need recent verions of Mage, Prekin, Probe, Reduce and Kin3Dcont, all of are available from our website:
You also need scoreDotsAtAtom, or a variant script, to count dots and format them for the contouring routines.


  1. First use Reduce to add hydrogens to the pdb file:
    reduce -build -penalty1 1gid >1gidH

  2. Then use Prekin to make a kinemage:
    prekin -lots -in 1gidH -out 1gidH.kin

  3. Probe makes the contact dots and we can append them to the kinemage:
    probe -mc -self altA 1gidH >> 1gidH.kin

  4. The .kin file can be viewed with Mage
    mage 1gidH.kin

  5. A script can run Probe in such a way that the number of dots for each atom is collected:
    scoreDotsAtAtom 1gidH >1gidH.scoreat

  6. Finally we can make a 3D countour, at several levels, plot of contact dot counts.
    kin3Dcont -kin -group 1gidH.scoreat -g1 -s2 -level 1.5 grey 2.5 brown 3.5 orange 4.5 gold > 1gidHcont.kin

    This last command wrote to a separate kinemage (rather than adding the contours to the end of the .kin file made above). To view it along with the structure, use the "Append" command in Mage under the "File" menu. To add the contours to the end of a previously created kinemage, drop the "-kin" flag and use the ">>" redirection symbol. Using ">" will overwrite any previous file, while ">>" appends.

J. Michael Word or
David C. Richardson
Biochemistry Department
Duke University
Durham, NC USA 27710