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

[<m0...@ya...>]

 Dear Bob,
Thank you so much for the adaptations you've put into Jmol for ConSurf.
My goal is to be able to support all the variations of .pdb file formats generated by ConSurf. I have a substantial collection of files processed by ConSurf going back more than a decade. Quite possibly other ConSurf users also have collections. The addition of REMARK 998 in the header section is a very recent addition. So it is missing in most of my collection. Therefore I will keep the code in FirstGlance that works around the various issues in earlier files.
With continuing gratitude, -Eric
    On Saturday, May 30, 2026 at 10:41:09 PM EDT, Robert Hanson <ha...@st...> wrote:  
 
 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.  


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