In PyMol, you can fetch/upload two PDB structures and ask it to align them. From this, you can extract the sequence alignment as well as structural alignment. We fetched the PDB structure of 2kmc (the TAs favorite protein) by downloading it from RCSB.org (2kmc.pdb), as well as imported its predicted structure that we downloaded from Alphafold (AF-P59113-F1-model_v4.pdb). 2kmc has structure for only part of the sequence (as was explained during recitation), whereas the Alphafold structure is for the full sequence. For your convenience, we downloaded a single pdb file that contains aligned structures. To quantify how good the predicted structure is, we may use a measure called RMSD, which stands for root mean squared distance. Though coordinates are given for every atom, the RMSD for protein structures is typically measured for only alpha carbon atoms. As the name RMSD indicates, it involves (i) computing distance between alpha-carbon atoms, (ii) squaring it, (iii) then finding mean of it, and (iv) then finding the square-root of the mean. Distance between two points whose coordinates are (x1, y1, z1) and (x2, y2, z2) is d = sqrt ((x2-x1)2 + (y2-y1)2 +(z2-z1)2) To compute (i) and (ii) above together, you can skip sqrt so that you directly have d2. So, find mean of d2 of all alpha carbon atoms and sqrt of mean. a) Compute RMSD of the aligned structures (align-full.pdb). You should include the residues that have records in both chains and ignore those that occur in only one. Paste RMSD value rounded to 3 digits after decimal below. Note that this measure is in Angstroms () because x, y, z coordinates are also in . ALIGN PDB: https://easyupload.io/ozdqxr