[Chimera-users] membrane boundaries

[Elaine Meng]

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: 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
...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:
<https://opm.phar.umich.edu/>

I hope this helps,
Elaine
-----
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