[Chimera-users] Trouble with Volume surface and active model not aligned

Phan Trieu Truong truongp at uga.edu
Fri Oct 20 14:05:37 PDT 2017

Hi Elaine,

I have tried the "reset" command. It works. Thank you very much!


From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Friday, October 20, 2017 4:41:34 PM
To: Phan Trieu Truong
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Trouble with Volume surface and active model not aligned

Hi Phan,
I’m not sure what happened either, since your images show the “A” (active for motion) boxes in the Model Panel are checked for both the molecule and the orbitals, meaning that using the mouse should move both of them together.

You could try command:
… to put them back together.

If that doesn’t work, you may have to start over by quitting and reopening the files.  However, if you didn’t uncheck the “A” boxes or the “Active models” boxes below the Command Line, mouse movements should always move them both together.  Maybe you accidentally had one of the A(ctive) boxes unchecked and moved the other model.  In that case, reset will work.
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 20, 2017, at 8:57 AM, Phan Trieu Truong <truongp at uga.edu> wrote:
> Hi,
> I have been using Chimera to visualize MO orbital on molecules from ORCA calculations. I have been able to visualize the MO orbitals as a surface volume from cube files. However, I just found out that when I try to reorient the molecule with the surface volume, they are no longer aligned. I don't know what I did to cause this. Any help is much appreciated.
> Attached is the picture of the molecules before and after I tried to reorient the molecule with the surface volume.
> Thank you,
> Phan
> <Before and after reorientation.jpg.png>_______________________________________________
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