[chimerax-users] using atomic coordinates to measure volume

Wed Dec 21 16:58:52 PST 2022

Hi Dan,

  Quantifying the packing density of molecules in a liquid mixture looks like a difficult statistical problem. The two things I can suggest to get some idea of density is to measure distances (water-water, ethanol-water, ethanol-ethanol). ChimeraX docs explain how. And on the ChimeraX recipes web site is a Python script that can make a convex hull surface using the center points of specified atoms. And ChimeraX can compute the volume in that surface. So you could for instance look at volumes of tetrahedra define by 4 packed waters or water-ethanol combinations. 

  Not sure how any of this will elucidate partial molar volume, where mixing water and ethanol occupies less volume then the water and ethanol separately. 

   Tom

> On Dec 21, 2022, at 11:15 AM, Eric Pettersen via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> I think you could select the water molecules of interest and the solute and then "surface sel enclose sel" to put a surface around them and then "measure volume" to report the volume enclosed by the surface.  If the waters and solute are in separate models, I think you would need to use the "combine" command to put them into one model because I don't think a surface computation works across multiple models.
> 
> --Eric
> 
>    Eric Pettersen
>    UCSF Computer Graphics Lab
> 
> 
>> On Dec 21, 2022, at 4:59 AM, Harrison, Daniel P via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Hello Tom,
>> 
>> Ah yes. The second case of liquid state calculation with random packing is closer to what I am working with. 
>> 
>> Here is my current process:
>> 1) Assuming the crystal structure of ice is a good model for liquid water, I took the crystal structure of ice and symmetry generated a 60-water molecule xyz coordinate file. 
>> 2) I took the xyz file to perform a very low level, PM3, optimization calculation with ORCA and the structure is relatively stable. (Note I will do higher level QM/MM calculations once I have fleshed out this method further). 
>> 3) Next, I replaced a water molecule in the center of this 60-molecule cluster with either methanol, ethanol, isopropanol, and tbutanol. With these I performed low-level optimization calculations. 
>> 4) Pleasingly, the water molecules reorient themselves and collapse around the alcohols to varying degrees. (As an aside, the optimization trajectory steps produce a nice "video" that one could interpret as liquid structure in motion.) 
>> 5) My objective is to quantify this collapse by having my students select some number oxygen atoms around the area of interest (i.e. around the alcohol) and calculate the volume made up by this "random" orientation of liquid water molecules with UCS ChimeraX. This is where I am failing.
>> 
>> Does this make sense? Do you have any suggestions either capturing the information I'm looking to acquire or on my process? 
>> 
>> Thank you greatly for your consideration and help!
>> 
>> Dan 
>> 
>> P.S. In the long run, I am hoping to add another dimension to this project by adding a virtual reality element with ChimeraX but that is down the road. 
>> 
>> 
>> 
>> -----Original Message-----
>> From: Tom Goddard <goddard at sonic.net> 
>> Sent: Tuesday, December 20, 2022 4:32 PM
>> To: Harrison, Daniel P <harrisondp at vmi.edu>
>> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
>> Subject: Re: [chimerax-users] using atomic coordinates to measure volume
>> 
>> Hi Daniel,
>> 
>> Is the idea for your partial molar volume calculation that you have crystals and want to find the fraction of the volume of a crystal unit cell that is occupied by the atoms?  Or are you trying to do a liquid state calculation where the atom positions would be packed randomly?
>> 
>>    Tom
>> 
>> 
>>>> On Dec 20, 2022, at 1:23 PM, Harrison, Daniel P via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>> 
>>> Thank you, Elaine!
>>> 
>>> I will take a look through your suggestions and let you know if I have any further questions. 
>>> 
>>> My "maximum" volume, I was envisioning that a number of plane-faces would need to be generated for the calculations and envisioned that that can be accomplished any number of ways. Maximum was referring to the space inside of the planes made by the largest polyhedron possible from all of these planes, though I admit that I am not an expert in this area. 
>>> 
>>> Best wishes and thank you again,
>>> Dan
>>> 
>>> 
>>> 
>>> -----Original Message-----
>>> From: Elaine Meng <meng at cgl.ucsf.edu>
>>> Sent: Monday, December 19, 2022 11:42 AM
>>> To: Harrison, Daniel P <harrisondp at vmi.edu>
>>> Cc: chimerax-users at cgl.ucsf.edu
>>> Subject: Re: [chimerax-users] using atomic coordinates to measure 
>>> volume
>>> 
>>> Hi Dan,
>>> I don't understand what you mean by "maximum" volume.  You can calculate a molecular surface that encloses the atoms (solvent-excluded surface based on their VDW radii) and then measure the volume enclosed by that surface.
>>> 
>>> "surface" command and solvent-excluded surface diagram 
>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>
>>> 
>>> For example, if the set of atoms is selected, command
>>> 
>>> surface sel enclose sel
>>> measure volume #1
>>> 
>>> ...assuming the structure and surface are opened as model #1.  If some other model number, substitute.  There is also a graphical interface to "measure volume," menu: Tools... Volume Data... Measure Volume and Area. For atomic models in angstrom coordinates, the reported volume will be angstroms cubed.
>>> 
>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume
>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/measurevolume.html>
>>> 
>>> ChimeraX only measures volume inside an enclosed surface.  It does not measure the volume of a pocket that is open to the exterior.
>>> 
>>> For pocket volumes, especially if open to exterior, you could try CASTp server, or 3Vee server to give a map that you could open in ChimeraX, show as isosurface, and then measure volume as described above.
>>> <http://sts.bioe.uic.edu/castp/calculation.html>
>>> <http://3vee.molmovdb.org/>
>>> 
>>> I hope this helps,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.                       
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry University of California, San 
>>> Francisco
>>> 
>>> 
>>>> On Dec 18, 2022, at 6:02 PM, Harrison, Daniel P via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>>> 
>>>> Hello: 
>>>> 
>>>> I would like to calculate the maximum volume made by selection of atoms in a given structure. Can you provide guidance on how to go about this process? It seems like there should be a simple procedure in ChimeraX but I have failed to locate it. 
>>>> 
>>>> My specific problem: I would like to calculate the volume of the void created by ice under various conditions so that my physical chemistry students can quantify and visually understand partial molal volume non-ideality.
>>>> 
>>>> I would greatly appreciate any assistance you can provide. 
>>>> 
>>>> Dan
>>> 
>>> 
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>> 
>> 
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