Hi Jianghai, Just wanted to note that there is some compensation for hydrogens even when they are not explicit. When there are no hydrogens, "united-atom" VDW radii are used (in surface area and other calculations) for the heavy atoms, in some cases bigger than when they do have explicit hydrogens. Details and values are given in the User Guide: <https://rbvi.ucsf.edu/chimerax/docs/user/radii.html> As far as I know, people usually don't add hydrogens before doing surface area calculations, especially since they are mostly used to compare one state versus another (different conformations or bound vs. unbound) rather than to get an absolute value. So it is more important to be consistent: either both states with hydrogens or both without. I hope this helps, Elaine

On Aug 27, 2026, at 10:54 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Jianghai,

The ChimeraX "measure sasa" command measures the solvent accessible of exactly the atoms you specify. If the structure does not have hydrogens then it doesn't include hydrogens. If you want the value with hydrogens then use the addh command to add the hydrogens. That command optimizes the hydrogen positions to make hydrogen bonds as described in the ChimeraX documentation (see the hbond option)

https://www.cgl.ucsf.edu/chimerax/docs/user/commands/addh.html

I guess there are cases where you want to see small changes in a large solvent accessible surface area, for instance if you consider alternate sidechain packing for just one residue. I added a precision option to the "measure sasa" command that will be in tonight's ChimeraX daily builds dated August 27, 2026 or newer.

measure sasa #1 precision 8

The new precision option says how many digits to print in the Log. It does not effect the accuracy of the calculation which is done using 64-bit floating point. The default output has 5 digits.

You can also change the number of digits in older ChimeraX by editing the Python code in your ChimeraX installation. For instance on Mac the file to change would be

ChimeraX-1.12.app/Contents/lib/python3.11/site-packages/chimerax/surface/measure_sasacmd.py

which has a line

msg = 'Solvent accessible area for %s = %.5g' % (aname, area)

that you could edit it a plain text editor to

msg = 'Solvent accessible area for %s = %.8g' % (aname, area)

to show 8 digits of precision. Due to security on newer macOS you would probably also have to give your editor permission to edit the ChimeraX application files using some Mac system settings.

Tom

...

On Aug 26, 2026, at 8:44 AM, jianghai.zhu--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

I'm using ChimeraX to calculate the solvent-accessible surface area (SASA) of a large complex. The output SASA is 6.1455e+05. It seems ChimeraX only outputs 5 digits. Is there a way in ChimeraX to output more digits, say one or two digits after the decimal point?

When calculating SASA or other areas, ChimeraX doesn't seem to compensate for hydrogens if there are no explicit hydrogen atoms in the pdb file. Is it better to use "addh" before "measure sasa"? As far as I can tell, ChimeraX doesn't optimize the orientation of riding hydrogens like other programs, such as phenix.reduce. Is that correct?

Thanks!

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Thanks, Elaine, for clarifying some of the details. I understand that the SASA difference between calculations with and without hydrogens is small. And it is true that many people only care about comparisons. However, technically speaking, the surface area calculated without hydrogens is NOT the true "solvent accessible area". I don't think there is a name for it. I do appreciate that in PISA, it always compensates for hydrogens when no explicit hydrogens are present in the structure; therefore, one gets the same answer with or without hydrogens in the pdb file. No confusion there.

That is what I understood as well, though I don't know which VDW radii (enhanced) PISA uses. I will have to dig into its source code to find out, since they aren't listed on the webpage. But PISA's calculation is simple because one gets the same answer with or without hydrogens. In ChimeraX, one can get an SASA for a structure without explicit hydrogens, but it is partially compensated for hydrogens. Alternatively, one can add hydrogens first and then calculate an SASA, which uses a different set of VDW radii and gives a different result from the first calculation. That is why my students are confused. I'm not saying there is something wrong with how ChimeraX handles the calculation. I just want to make sure I understand what is going on here.