[chimerax-users] trying to make molmap surface similar to molecular surface

[Elaine Meng]

Hi Yaikhomba,
There is no exact equivalent, as the ways in which the molecular surface and map (from molmap) contour surface are calculated are totally different.

However, I have experimented with trying to get a (very approximately) similar look and position of those two kinds of surfaces in Chimera,  and there is an example of molmap with those parameters as workaround #3 in the Chimera surface workarounds page:

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>

I do not recall the contour level used, and it might vary depending on the structure, so you probably still have to adjust the volume threshold (map contour level) to try to make the contour close to where the molecular surface lies.  

In summary:  There isn't any reason to use molmap if the goal is to get something similar to the molecular surface.... just use the molecular surface.

Another issue with molmap is that you have to be careful to only include the protein atoms, or else it may include ligand, solvent, etc. that would not be included if you had used the regular molecular surface approach.

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

> On Nov 27, 2020, at 1:57 PM, Y. Mutum <ym337 at cam.ac.uk> wrote:
> 
> Hi Elaine
> 
> Thanks - will try this.
> On this note, I had a quick question on the molmap command.
> 
> What is the molmap (contour threshold and resolution values) equivalent to in terms of the Surface generated from a pdb file?
> 
> To paraphrase - how can we make the surface generated from 'molmap command' resemble the one generated from the 'surface command' ?
> 
> I might not be very accurate here, as molmap generates a volume, but say my question refers to the surface of the volume generated.
> 
> Thanks
> Yaikhomba