Re: [Jmol-users] Blank temperatures + ANISOU generate spurious temperature values

[Robert H. <ha...@st...>]

This is not necessary. Just use Jmol as it is.

On Sat, May 30, 2026, 12:49 PM m0...@ya... <m0...@ya...> wrote:

> Yes, Bob, what you have done in 16.4.3 seems a good solution. Thanks!
> Also, FirstGlance now (i) determines which chain (and sequence-identical
> chains) have ConSurf conservation grades, and then (ii) zeros temperature
> values for all other atoms, which also takes care of the problem.
>
> Thanks for explaining how ANISOU generates temperature values.
>
> -Eric
>
>
>
> On Saturday, May 30, 2026 at 12:01:06 AM EDT, Robert Hanson <
> ha...@st...> wrote:
>
>
> Eric, ask the folks at consurf to remove the ANISOU records. By co-opting
> the isotropic b-factor, they have destroyed the anisotropic parameters
> anyway, because that number is the isotropic b-factor. Without that number
> -- just for some values now -- Jmol approximates the isotropic b-factor
> from the anisotropic parameters. But according to Google AI, this is not
> reliable, because during refinement, the temperature factor (B_iso) and the
> anisotropic parameters can get out of sync.
>
> [image: image.png]
>
> So we have two problems:
>
> 1) Jmol uses the consurf values for "temperatures" when they are there.
> 2) Jmol approximates the B_iso value from the ANISOU records as best it
> can when the b-factor is not there.
>
> Jmol 16.4.3 is reading the REMARK 998 line, and when that has "ConSurf" in
> it, it foregos approximating B_iso values.
>
> Eric, does this solve your problem?
>
> Bob
>