Make button to update metal coordination bonds

[wilian.cortopassi@…]

Would like a way to update metal coordination bonds when atoms of a structure are moved with the move selected atoms mouse mode.

On Feb 20, 2020, at 5:00 PM, Cortopassi, Wilian wrote:

Hi Tom,

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Some additional feedback:

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(iii) When I open the pdb 6N2Y, it automatically displays an interaction between the phosphate group and the magnesium. Then, when I use the "move atoms" functionality, this interaction is still there all the time, which looks quite weird, since the ATP and the magnesium would be very far from each other. I think this is in line with the question in topic (i) - when we do modify the protein/ligand, is there a quick way for the nearby environment to quickly adjust to these changes?

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[Eric Pettersen]

Chimera 1 has a "Metal Geometry" tool capable of identifying atoms coordinating a metal and updating a metal-coordination pseudobond group. ChimeraX does not have that. If the coordination bonds are present in PDB input, ChimeraX does have the ability to identify which bonds are in fact metal-coordination bonds and convert those into the appropriate pseudobonds, but no ability to identify them if the bonds aren't already present.