Thank you so much Elaine! Very helpfull explanation about how to use match! Despite that, I have a problem with some match and selection. For some protein when I type for example: match #0:346@n,ca,o,c #1:23@n,ca,o,c to match those atoms in position 346 and 23, chimera tells me that the number of atoms is not the same. How this is possible? Thank again. -- Alessandra Gastaldello
Hi Allessandra, You’re welcome! You would have to check specifically, but some reasons for different or unexpected numbers of atoms are: (1) a model has multiple chains, so that if you just say residue 23, there might be residue 23 in chain A, residue 23 in chain B, … to avoid this, just specify the chain directly. You can see which chains you have by putting the mouse over the structure and it will be shown in the pop-up information. For residue 23 in chain A only: #1.23.A@n,ca,c,o (2) one or more of the atoms is missing from a structure (3) structure has alternate locations of atoms, e.g. two positions of the same atom. If there were locations A and B, you could first delete all the “B” locations in all structures with: delete @.b (4) residue number is incorrect so it did not specify any atoms Some ways to check are by trying to display all those atoms, for example: ~ribbon disp #0:346@n,ca,c,o #1:23@n,ca,c,o (hiding ribbon allows showing backbone atoms) You can also try selecting either set of atoms, for example: select #0:346@n,ca,c,o … and then see how many atoms are selected, such as by clicking the green magnifying glass in the bottom right corner to open the Selection Inspector. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco