Hi Elaine and Eric,

Thank you for your answers!

Would be great to always label metals and halogens as ions, not solvent. By the way, in the solvent definition it says "not covalently bonded to other residues", but those calcium ions all have a "link" record/connection  type "metalc".

Kind regards,
Ute

From: Eric Pettersen <pett@cgl.ucsf.edu>
Sent: Thursday, December 4, 2025 19:59
To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>; Elaine Meng <meng@cgl.ucsf.edu>
Cc: Ute Roehrig <Ute.Roehrig@sib.swiss>
Subject: Re: [chimerax-users] Calcium ions labeled as solvent, not as ions
 
We could possibly change the solvent heuristic to exclude metal and halogen ions.

--Eric

        Eric Pettersen
        UCSF Computer Graphics Lab


> On Dec 4, 2025, at 10:44 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hi Ute,
> Interesting... this misclassification is due to the characteristics of this structure combined with the limitations of using heuristics to define solvent, namely:
>
> Solvent:  of the following two, the set with the greater number of residues:
>
>    • “small solvent” candidate set: residues of up to 3 atoms named WAT, HOH, and DOD, plus singleton atoms (i.e., not covalently bonded to other atoms) of atomic number 6-8 in single-atom residues
>
>    • “other solvent” candidate set: excluding residues in the “small solvent” set, the most prevalent type of residue that is not covalently bonded to other residues, has ≤ 10 atoms per residue, and is present in at least 10 copies in the structure
>
> (as documented here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#builtin>)
>
> Apparently the Ca++ are guessed as solvent because there are >10 them and the structure also does not have explicit waters.
>
> Regards,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>> On Dec 4, 2025, at 12:19 AM, Ute Roehrig via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>>
>> Hello,
>>
>> I am not sure if this is a problem in the structure or in ChimeraX or intentional, but I remarked that in PDB structure 7tba the calcium ions are labeled as "solvent" and not as "ions", although the element and atom type seem to be OK. I did not see the same in other PDB structures with calcium.
>>
>> Thank you for your help,
>> Ute
>
>
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