Hi I-Ji -

You say the superimposed atoms are still there; that seems like normal behavior to me.  If you disable one of the objects, can you see the other one, and vice versa?

If the two structures are nearly identical, you may not be able to differentiate them visually after alignment.  If that is the case, you may wish to use different representations and/or colors for the two objects.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On May 26, 2014, at 6:58 PM, I-Ji Jung <u5205176@anu.edu.au> wrote:

Hi,

I'm trying to superimpose a small structure to a residue of a protein.
When I use align or pair_fit to do this, the superposition works, but for some weird reason I can't see my small structure anymore. Like it's whole structure disappears. The superimposed atoms are there - but then those are overlapped by the same atoms of the residue, so you can't see them anyway. I've tried pair_fit some while ago and I recall using it without a problem. Why am I suddenly having this problem?
Can somebody help me?

Thanks,

I-Ji
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