int -> pdb conversion

Bernard Murray bpmurray*STUFFER* at socrates.ucsf.edu
Fri Jul 10 17:03:59 EST 1998


In article <dumbo-1007982133440001 at nostromo.bmc.uu.se>,
dumbo at xray.bmc.uu.se (Dombo Journal (Est. 1893)) wrote:

> In article <3PQIT1$qem at bbs.life.nthu.edu.tw>,
> mjhsieh.bbs at bbs.life.nthu.edu.tw (Á©sèû) wrote:

> ;->Seems that dihedral angle can't exactly determine the coordinate. :-)

> 
> (1) for internal coordinates to work, you'll need bond lengths,
>     bond angles, and dihedral angles - if you assume "ideal"
>     values for bond lengths and angles, errors will accumulate
>     and once you get to the C-terminus the result may be quite
>     large


(This thread is becoming more informative than I first thought)

I was just wondering....  Has anyone actually looked at the
variation in bond lengths from "ideal" in the protein
structure databases? (I realise the publication for individual
structures usually comment on strange bonds).  Are there any
publications on this?  It sounds like valuable information
for the databases for protein dynamics simulation.
     Just curious,
          Bernard
-- 
Bernard Murray, PhD
Dept. Cell. Mol. Pharmacol., UCSF, San Francisco, USA




More information about the Bio-soft mailing list