AMBER Archive (2002)

Subject: image command

From: Sophia Kondratova (x357l_at_unb.ca)
Date: Thu Aug 29 2002 - 12:46:01 CDT

When using the image command of ptraj, what is the most common or right way to
image: bymol (which is the default) or byatom, byres ... I have tried using
bymol imaging and the box still looked misshaped, but when I used the byatom
or byres imaging, the box seems to look better. What is the difference between
the three choices and when should each one be used? Also if I have a
rectangular parallelopiped, should I use the familiar command?

Thanks a lot for any help.

Sophia Kondratova