[Chimera-users] Possible bug?

Hernando J Sosa hernando.sosa at einstein.yu.edu
Tue Oct 31 14:54:59 PDT 2017

  With the latest Chimera version (1.12) I get an error message after saving a file.  The error says that the file does not exist (the file didn't exist as it is being created new).  The file is saved OK though.



-----Original Message-----
From: Chimera-users [mailto:chimera-users-bounces at cgl.ucsf.edu] On Behalf Of Elaine Meng
Sent: Tuesday, October 31, 2017 4:20 PM
To: James Starlight
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] Axes/Planes/Centroids for the OPM membrane visualization

Hi Gleb,
If you define a plane it will be a plane (a flat circular disk), but it does have a slight thickness, so maybe that is what you meant by “cylindrical."

If you are trying to do something similar to this image, <http://www.rbvi.ucsf.edu/chimera/ImageGallery/entries/dopamineReceptor/dopamineReceptor.html>

...you would have to define two planes, one for the outer membrane and one for the inner membrane. In the files from OPM, even though all the “membrane” points are residue DUM, different atom names are used for the inner and outer leaflets:  O for the outer and N for the inner.  So you can select one set of points or the other with commands like:

select :dum at o
select :dum at n

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 31, 2017, at 10:27 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> Dear Chimera Users,
> I have a question regarding Axes/Planes/Centroids for the 
> visualization of the membrane plane predicted by OPM.
> Firstly, I have uploaded my structure with DUM atoms. Than, I selected 
> the DUM atoms in both layers and try to show the membrane plane via 
> defining of a plane for it. As the result, a cylindrical surface 
> oriented perpendicular to the imaginative membrane has been emerged.
> What should I change in options to obtain it aligned along the 
> membrane normal in a correct way? Is it possible to make more flexible 
> selection of the DUM atoms only in the selected layer?
> Thank you for the help!
> Gleb

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