[Chimera-users] Substrate channel identification for homotrimer protein

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 5 08:01:36 PDT 2019

Hi Joydeep,
You could try asking the developers of those tools.  On their websites there are contact e-mail addresses:



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

> On Apr 4, 2019, at 7:04 PM, Chakraborty, Joydeep <jc323 at njit.edu> wrote:
> Hello
>  I was trying to generate the substrate channel including the substrate binding pocket for my enzyme using the 3V channel finder server. On setting the outer probe radius to 9 Å and inner probe almost the same as that of a water molecule, 1.5 Å, the software was able to generate very accurately the solvent accessible substrate channel, that matches the crystallography reference. The mrc file can be opened together with the pdb file in chimera to generate a similar image that I have attached for reference. 
>  However, my protein happens to be a homotrimer and theoretically it should have 3 substrate channels. Having said this, I have a general question for the community. Can anyone shed some light on the fact why 3V server does generate just one channel for the trimer instead of three?
>  Since, very simply the server uses a rolling sphere (1.5 Å radii) to detect the cavity, I am curious as to why only one channel is shown. Also, the same thing happens with CastP that generates one substrate pocket for an entire protein irrespective of a trimer or a dimer. Since, my computational knowledge is quite limited being from a wet lab background, any feedback on this would be much appreciated.
> Thanks!
> With regards,
> Joydeep.

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