I have a pdb file of RuBisCO enzyme (8RUC) binds with 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE (C6 H14 O13 P2). I want to replace C atom and two oxygen atoms bound to the seconds Carbon of the ligand (2C) with an OH. This atom replace part can be done using chimera. But I cannot find a way to add a double bond to 2 and 3 Carbon atoms. Please give me a solution.
As far as I know, there is no specification in a pdb file to indicate bond order. That is usually done in the Molecular Viewing software (by using the bond length). The free software Avogadro may be able to help you, because with it you can change bond order and do a MM optimization, which will shorten the bond. It sounds like you are going to do something else with this structure that will require a double bond???
Other file types have the bond order coded in them if you are saving into a different format.
Is this for visualization purpose or simulation?
For simulation you don't need to change anything in pdb file for double bonds. the potential you assign to that bond should carry required parameters to handle that.
If this is for visualization purposes, in every software you use, there should be a section to customize selected bonds as double bonds.
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