Subject: CCL:X-Ray to Cartesian conversion

From: Stefan Seidler <[email-masked]>
Date: Wed, 22 Nov 2000 17:04:27 +0100 (MET)

Hi Tapan,

the header for the babel "Free format fractional coordinates" is as follows
(from babel file rdfract.c function read_fform_fract()):

no_atoms alpha beta gamma a b c
empty_line
atomsymb fx fy fz
...

The conversion from fractional to cartesian coordinates is perfect,
but to get one connected molecule as you may expect you need to adjust the
fractional coordinates. To take into account the translational periodicity 
add and subtract multiples of 1 to the x y and z fractional coordinates.

The easiest way is to automatically build a "crystal" by a programm 
(CRYSIN command in Sybyl or Solids_Builder in InsighII) and extract a single 
complete structure. 

A set of cartesian coordinates for your -CH2-C5H4N are: 

N1   4.8742    2.9112	 2.3771 
C4   5.2707    3.2356	 1.1710 
H4   4.8664    3.9619	 0.7560
C7   6.4145    1.0996	 2.3201 
H7   6.7854    0.3719	 2.7636
C8   5.4149    1.8571	 2.9213 
H8   5.1186    1.5976	 3.7637 
C5   6.2654    2.5530	 0.4749 
H5   6.5332    2.8426	-0.3666 
C6   6.8454    1.4461	 1.0456 
C9   7.8370    0.5940	 0.3343 
H9A  8.2900    1.1352	-0.3305 
H9B  8.5040    0.2966	 0.9725 

Hope this helps,

   Stefan
   
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