[Chimera-users] Volume subtraction of surface area between homology model and template

[Elaine Meng]

One clarification:  for atomic structures, Chimera and ChimeraX display the solvent-excluded surface (SES).  Chimera gives areas for both SES and SAS (solvent-accessible surface) in the Reply Log, whereas ChimeraX can only report the SAS area, with command "measure sasa."

The ChimeraX "surface" help has a diagram showing the difference between SES and SAS:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>

Elaine

> On Jul 6, 2021, at 9:49 AM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Nick,
> It sounds like you are using ChimeraX, not Chimera.  (ChimeraX has "volume subtract" whereas Chimera has "vop subtract"... there is a different address for asking chimerax questions, chimerax-users at cgl.ucsf.edu)   Next time please be sure to check or at least clarify which program you're using so I don't have to answer for both programs, since they are somewhat different.
> 
> (1) In Chimera:
> The surface areas are reported when you show the surfaces.  So if you literally wanted the difference in surface area (not volume) just subtract the surface areas reported in the Reply Log when the surfaces are first shown.
> 
> To measure a surface-enclosed volume, it's command "measure volume" or Tools... Volume Data... Measure Volume and Area. See:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html>
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/measurevol/measurevol.html>
> 
> (2) In ChimeraX:
> The surface areas are not reported automatically, but you can use commands "measure volume" and "measure surface" and (for atomic structures) "measure sasa"
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html>
> 
> Those would just give you single numbers (total quantities), not a "difference density."  A molecular surface is not a map, i.e. it's not an isosurface determined from density values.
> 
> For a difference density map you would have to use molmap and volume subtract, like you already described.
> 
> Alternatively you could just display both molecular surfaces, perhaps as mesh or making one of them transparent (both transparent will not work right).  If you just want a visual, that is probably the way to go, since the molmap isosurface is not the same as the solvent-accessible molecular surface.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Jul 6, 2021, at 8:54 AM, Kovacs, Nicholas (CDC/DDID/NCIRD/ID) via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Hello,
>> I have a homology model that I have made and I would like to create a visual that portrays small surfaces where there is change in the solvent accessible surface area of the homology model compared to the template structure. I am trying to use the “subtract” map from map calculation which requires volume data for the 2 structures. I have tried the following to generate volume data and then subtract the volumes, but I am getting hundreds of small surfaces all throughout the area of the molecule:
>> 
>> molmap #1 3
>> molmap #2 3
>> volume subtract #3 #4
>> 
>> I know molmap is likely not the command I want to be using since I am interested in the solvent accessible surface area but I have yet to find a command that will generate a volume corresponding to the volume enclosed by the solvent accessible surface area. I would greatly appreciate it if someone could help me find a way to create 2 volumes enclosed by the solvent accessible surface area of the 2 structures in addition to correctly configuring the “volume subtract” command to get my desired output. 
>> Thank you,
>> Nick
> 
> 
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