Hi Mariam, If you know the X,Y,Z location in your structure where you want the calcium, you can add an atom with the Build Structure tool (in menu under Tools... Structure Editing) , Start Structure section, option Add: atom. This atom will be helium but you can change it to calcium with the Modify Structure section of the same tool. See Build Structure help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#top> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#start> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#modify> - OR - If you do not know the X,Y,Z location, but there is some similar structure in the PDB that includes the calcium, you can open that other structure, match onto your alphafold structure, then delete everything from the other structure except the calcium, and then combine the calcium with your alphafold structure. In detail: (1) open the other structure (2) superimpose the two structures, e.g. with matchmaker tool (in menu under Tools... Structure Analysis) or command, e.g. if your alphafold model is #1 and the other structure is #2, command: mm #2 to #1 If this works to superimpose the area where the calcium is supposed to be bound, go on to step 3. If it does not, you may instead have to do one or more of the following to get that part superimposed well: select only the parts you want to use for the matchmaker fit and check the option(s in Matchmaker to "also restrict to selection", or use the "align" command to say exactly which atoms to fit when superimposing the structures, or use the mouse to manually move one structure or the other. See <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#selective> (3) delete everything in the other structure except the calcium. For example, if your alphafold model is #1 and the other structure is #2 you can select the calcium ion (Ctrl-click on the atom) and then use command to delete all the atoms in #2 except the selected atom: delete #2 & ~ sel (4) combine the two models to make a new model #3 that is all the atoms from both, e.g. command: combine #1,2 model #3 See <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> If #3 looks like it has what you want then you can close the others, e.g. close #1,2 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 16, 2024, at 4:38 AM, MARIAM ALZAABI via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Sir,
How to add calcium ions into a predicted protein structure that I created using alpha fold colab in chimeraX
Thank you.