[Chimera-users] membrane boundaries

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 12 09:48:35 PDT 2019

Hi Anaswara,
Chimera does not have a tool specifically to identify the membrane boundaries.  As a clue to figuring it out yourself if you have an atomic structure of the protein, you could display amino acid hydrophobicity on the surface, for example as in this tutorial: 
...but it would not guess a boundary for you.

Outside of Chimera:
Thanks to Tamas for his suggestion, for cryoEM maps!  

Another thing that might be useful for atomic structures is the Orientations of Proteins in Membranes database:

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

> On Mar 12, 2019, at 9:06 AM, Tamas Hegedus <tamas at hegelab.org> wrote:
> Hi,
> Could you give more specification what a where do you want?
> We just resubmitted our manuscript on determination of membrane boundaries from cryo-EM densities. You can try our web app:
> http://memblob.hegelab.org
> Please provide feedback on bugs.
> Thanks,
> Tamas
> On 3/12/19 3:54 PM, Anaswara Ashok wrote:
>> Hi
>>  I would like to know if we could add membrane boundaries of proteins with chimera?
>> -- 
>> Regards
>> Anaswara Ashok
> -- 
> Tamas Hegedus, PhD
> Senior Research Fellow
> Department of Biophysics and Radiation Biology
> Semmelweis University     | phone: (36) 1-459 1500/60233
> Tuzolto utca 37-47        | mailto:tamas at hegelab.org
> Budapest, 1094, Hungary   | http://www.hegelab.org

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