[chimerax-users] vdw representation in chimeraX

[Elaine Meng]

> On Sep 9, 2019, at 3:29 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Elena,
> There isn’t an equivalent command in ChimeraX.  You can show the molecular surface as dots (command: surface; surface style dot) but it is the  solvent-excluded surface, not dots.

Haha, that should be “solvent-excluded surface, not the VDW surface”
Elaine

>  If you show the atoms as spheres, their surface is the VDW surface (command: show atoms; style sphere), but it is not dots.  
> 
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/style.html>
> 
> Technically, it IS possible but impractical if you want to do it on many atoms: using the command “surface” many, many times with the option “enclose” you could make a surface enclosing each atom individually, and then use “surface style dot” as mentioned above, but it would be extremely tedious.  It probably would not look how you wanted it to look.  The dots are very tiny, with no option to make them larger, and to make the dots closer together you would have to use a small “gridSpacing” value and it could become computationally expensive (slow to rotate the molecule).
> 
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Sep 9, 2019, at 2:18 PM, Elena Zehr <zehr.elena at gmail.com> wrote:
>> 
>> Hello,
>> In chimera one can display dot van der Waals surfaces for atoms. 
>> vdw atom-spec
>> What would be the equivalent command in ChimeraX?
>> Thank you,
>> Elena