Changes between Version 554 and Version 555 of ChangeLog

Timestamp:

Dec 15, 2025, 8:59:45 AM (2 days ago)

Author:

Elaine Meng

Comment:

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ChangeLog

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 This log includes significant new features of interest to users. Smaller enhancements, minor feature additions, and minor bug fixes are usually not included. Dates are approximate.
 
-December 11, 2025: ** Find Cavities options ** - two options have been added for more control over the [http://www.rbvi.ucsf.edu/chimerax/docs/user/tools/findcavities.html Find Cavities] search.  One for incorporating non-polymeric residues into the receptor surface (''e.g.'' prosthetic groups) and another for restricting the search to a box around a specific set of atoms (including optional padding).  There are corresponding options to the `kvfinder` command (`includeAtoms`, `boxAtoms`, and `boxPad`).
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-December 9, 2025: ** Alignment residue prevalence ** - the change in prevalence of chosen sequences relative to the entire alignment can be shown via [http://www.rbvi.ucsf.edu/chimerax/docs/user/tools/profilegrid.html Profile Grid]'s Chosen Cells→Change in Prevalence... context menu item. 
+December 11, 2025: ** Find Cavities options ** - new [http://www.rbvi.ucsf.edu/chimerax/docs/user/tools/findcavities.html Find Cavities] search options to include non-biopolymer residues (such as cofactors) in the receptor surface, and to restrict the search to a box around a specific set of atoms (including optional padding). There are corresponding options to the `kvfinder` command (`includeAtoms`, `boxAtoms`, and `boxPad`).
+
+December 9, 2025: ** Alignment residue prevalence ** - changes in the residue-type prevalences of chosen sequences relative to the entire alignment can be shown with the [http://www.rbvi.ucsf.edu/chimerax/docs/user/tools/profilegrid.html Profile Grid] context menu: Chosen Cells→Change in Prevalence... 
 
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