Re: [ccp4bb]: Protein Dimensions

[Luca Jovine <jovinl02@doc.mssm.edu>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***

>What is the best way to determine a proteins dimensions from the three
>dimensional structure?  I could just measure from end to end at the
>widest point (between CA's) in Xfit, but is there a better method that
>would take into account a Van der Waals surface or something similar.

There might be better ways, but:

1) within CNS, you can use the input file molecule_extent.inp, which 
"Determines the extent of a molecule in orthogonal Angstroms"

2) in WHATIF, you can use the command MINMAX which determines the 
extreme values for the coordinates within a user-specified range

Hope this helps, Luca
-- 
--------------------------------------------------------------------------------
  Luca Jovine, Ph.D.
  Department of Biochemistry and Molecular Biology
  Mount Sinai School of Medicine
  Annenberg Building, Room 25-18
  One Gustave L. Levy Place, New York, NY 10029-6574, U.S.A.
  Voice: +1.212.241-8620  FAX: +1.509.356-2832
  E-Mail: jovinl02@doc.mssm.edu  W3: http://www.mssm.edu/students/jovinl02
--------------------------------------------------------------------------------