<s>
It	O
can	O
be	O
used	O
for	O
scientific	B-Application
visualization	I-Application
and	O
analysis	O
,	O
and	O
chemistry	O
and	O
biology	O
instruction	O
.	O
</s>
<s>
The	O
set	O
of	O
commands	O
has	O
been	O
patterned	O
after	O
RasMol	B-Language
,	O
so	O
it	O
's	O
fully	O
compatible	O
with	O
extant	O
scripts	O
.	O
</s>
<s>
Extant	O
RasMol	B-Language
scripts	O
can	O
be	O
imported	O
and	O
run	O
within	O
Sirius	O
to	O
produce	O
high	O
quality	O
representations	O
of	O
encoded	O
molecular	O
scenes	O
.	O
</s>
<s>
Since	O
RasMol	B-Language
uses	O
a	O
coordinate	O
system	O
that	O
differs	O
from	O
that	O
Sirius	O
,	O
internal	O
conversion	O
is	O
performed	O
when	O
RasMol	B-Language
scripts	O
are	O
imported	O
,	O
so	O
that	O
any	O
orientation	O
changes	O
are	O
shown	O
correctly	O
.	O
</s>
<s>
It	O
can	O
read	O
output	O
files	O
from	O
AMBER	B-Device
and	O
CHARMM	B-Application
simulations	O
,	O
including	O
compressed	O
and	O
AMBER	B-Device
out	O
files	O
.	O
</s>
<s>
RMSD	B-General_Concept
changes	O
along	O
the	O
trajectory	O
can	O
be	O
calculated	O
using	O
user-defined	O
atom	O
subsets	O
and	O
displayed	O
in	O
an	O
interactively	O
updated	O
graph	O
.	O
</s>
<s>
The	O
full	O
trajectory	O
or	O
selected	O
frames	O
can	O
be	O
exported	O
as	O
QuickTime	B-Application
video	O
or	O
a	O
set	O
of	O
POV-Ray	B-Application
scene	O
snapshots	O
that	O
can	O
later	O
be	O
converted	O
to	O
a	O
high	O
quality	O
movie	O
.	O
</s>
<s>
Native	O
desktop	O
application	O
installers	O
are	O
available	O
for	O
Windows	B-Application
,	O
Linux	B-Application
,	O
and	O
macOS	B-Application
.	O
</s>
