From chemistry-request@ccl.net Fri Apr 24 15:36:17 1992
Date: Fri, 24 Apr 92 16:20 N
From: NMRGENT%LOS.RUG.AC.BE@OHSTVMA.ACS.OHIO-STATE.EDU
Subject: how to define and calculate a helix axis
To: chemistry@ccl.net
Status: RO

  Hi,

     I have calculated a number of n.m.r structures for a 31
     residue polypeptide toxin, using the variable target function
     program DIANA.One of it's structural features is an alfa helix
     that spans 10 residues(2 1/2 turns).However from average phi psi
     values it is clear that the helix is distorted from standard
     geometry.This causes the helix to appear 'bananashaped'.I guess
     the best way to describe this shape would be to compare the
     axis of the helix with that one of a helix with standard geometry
     So here it comes.What is the definition of a helix axis, and how
     can it be calculated from for instance cartesian coordinates of
     the backbone atoms? I use Insight/Discover software from biosym
     to visualise my results,so a program using car files or pdb type
     files would be welcome if available.

                            Hope somebody out there likes me!!!

                             Jose Martins,
                              NMR Dept.
                              Lab. Org. Chem
                              University Gent
                              Belgium
                              NMRGENT@LOS.RUG.AC.BE


Belgium, a french,german and dutch speaking country, where scientist
  have to speak englisch to understand each other!!!

From chemistry-request@ccl.net Fri Apr 24 16:30:45 1992
Date: 24 Apr 92 14:13:48 GMT
From: Siegfried.Schneider@CNVE.RRZE.uni-erlangen.de
To: CHEMISTRY@ccl.net
Status: RO

I developed a program, which might be of interest for those who prefer
to write there Z-matrices by hand.
One of the mayor disadvantages of using a conventional Z-matrix as an input
for Mopac-calculations is the necessity to keep track of the numbering of
the used atoms. This can get quite tricky in case of very large molecules.
Another problem frequently encountered is if one wants to substitute parts
of a molecule by other substituents.
The program enables the user to split a molecule into fragments, defining
the Z-matrix for each fragment separately and putting fragments together by
defining postions of a fragment relative to another fragment. (Hope everyone
understands what I mean)
Also it is possible to use an archive of fragments, so that frequently used
groups (e.g. methyl of phenyl) can be incorporated easily.
Another application would be the study of a complex of two molecules or
a molecule surrounded by a solvent.

The benefits of the program are:
  o The construction of a Z-matrix even for larger molecules is much easier,
    without recoursing to computer programs like PC-model.
  o Substituting fragments of a molecule by different fragments, does not
    require a recalculation of the referenced atomsnumbers. Also the atoms
    of a fragment are not spread over the whole input-file.
  o By using an archive of fragments, it is not necessary to reconstruct
    frequently needed fragments again and again. (e.g. Methyl- or
    phenylgroups)

The program is written in C and was tested on a PC an a workstation.

Whoever is interested in this program can get it from me.
Just send a letter and I will post the source-code.

Peter Gedeck



Peter Gedeck
Inst.f.Phys.Chem. 1
Egerlandstr. 3
8520 Erlangen

FAX 09131 - 858307
E-mail : PC1@cnve.rrze.uni-erlangen.dbp.de