Oscail likes to use SHELX INS files but almost any type of XYZ coordinate
file may be used. The Formats file conversion program can deal with most of the
common file types. If you can find no source for the molecule you want then
build it in a molecular modeler and try to export some type of coordinate file. Moilin
(the molecular modelling part of Oscail) can be used to build a molecule (with Tinker,
Mopac, Gamess and Iconc optimization).
The following set of coordinates were taken from a web page.
The file had trailing atom names and was converted to the most basic format
that Formats can read (ATM format) as follows.
In the web browser the text was copied from the web page to the clipboard
Oscail.was
started and
clicked to start PFE.
In PFE initial atom names were added.
The ATM
format is just atom name followed by x,y,z. (The first line should be CELL a b c
alpha beta gamma if the coordinates are fractional)
o 1.0562 0.9066 5.8333 O
c 1.5532 1.4480 4.8746 C
c 2.0226 0.6120 3.6925 C
o 1.7066 2.9633 4.8556 O
c 3.4870 0.8662 3.3742 C
c 1.6595 -0.8892 3.8040 C
c 1.0919 0.6956 2.4577 C
pt 3.4577 3.9591 4.2620 PT
o 4.2423 -0.0738 3.3015 O
o 4.0343 2.2781 3.1429 O
c 1.2151 -0.8420 2.3214 C
n 2.9086 5.7250 5.2570 N
n 5.1796 5.0459 3.7235 N
h 0.8159 -1.0404 4.4612 H
h 2.5430 -1.4977 3.9289 H
h 1.5761 1.2018 1.6358 H
h 0.0906 0.9848 2.7409 H
h 0.2472 -1.3022 2.1877 H
h 2.0253 -1.1129 1.6607 H
h 3.4933 6.4985 5.2305 H
h 2.0703 5.7672 5.7432 H
h 5.8555 4.6363 3.1611 H
h 5.2967 5.9561 4.0378 H
The file was then saved as newjob.atm
In windows explorer double click newjob.atm and Oscail should start
with the correct Jobname and Current Directory on the status line.
Click and select Formats
Select ATM >>>> INS / TEST.INS and check Overwrite INS then click OK and
select EXIT (bottom left) and OK
Click to start ORTEX and you should get
a picture. The above coordinates gave the following picture.