README.mapvol Home Page: Richardsons' Laboratory J. Michael Word - 8/1999


Mapvol is an awk script which reads a PDB file and tries to assign a volume to each atom based on residue and atom names. The output is a table, listing the volume and the atomic coordinates, which can be contoured with Kin3Dcont to show the distribution of atomic volume in a protein.

Set-Up


You will need recent verions of Mage, Prekin, Probe, Reduce and Kin3Dcont, all of are available from our website:
http://kinemage.biochem.duke.edu/
You also need the script mapvol, which works with

Mapvol comes in two components, a UNIX shell script which calls Bndlst and awk. Because of its size, the actual awk script is provided separately. When you decide where you will put mapvol.awk, change mapvol to make it refer to the awk script by its full name.

Usage


  1. Mapvol expects hydrogens in the PDB file. Use Reduce to add them:
    reduce -build 1gid >1gidH

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

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

  4. A script can run probe in such a way that the number of dots for each atom is collected:
    mapvol 1gidH >1gidH.atvol

  5. Finally we can make a 3D countour, at several levels, plot of contact dot counts:
    kin3Dcont -kin -group 1gidH.atvol -g1 -s2 -level .3 grey .35 brown .4 orange .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.


e-mail:
J. Michael Word or
David C. Richardson
URL: http://kinemage.biochem.duke.edu
Biochemistry Department
Duke University
Durham, NC USA 27710