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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