Hi Elaine, Thanks for your detailed instructions. My apologies for the confusion but your guess about the different models is correct. After following your instructions, I compared the first residue of the original PDB file with the first residue of 'model 2 (residues missing in chain A)' and following is what I got. Note, the x, y, z coordinates of the atoms have changed and the sequence of atoms has changed. I am not sure why this happens. Can you help me understand? Note, the missing residues where added in model 2 but I am not showing here as there is nothing to compare against. The coordinates for chain A of the first residue in original PDB file: ATOM 1 N CYS A 1 32.449 -7.381 50.051 1.00 18.85 N ATOM 2 CA CYS A 1 31.974 -7.012 48.720 1.00 17.01 C ATOM 3 C CYS A 1 33.101 -6.917 47.728 1.00 15.67 C ATOM 4 O CYS A 1 34.254 -6.671 48.116 1.00 16.39 O ATOM 5 CB CYS A 1 31.253 -5.658 48.764 1.00 17.77 C ATOM 6 SG CYS A 1 32.167 -4.263 49.459 1.00 19.16 S The coordinates for chain A of the first residue in PDB file after adding missing residues using Chimera-Modeller: ATOM 1 N CYS 1 32.426 -7.418 50.092 1.00 0.00 N ATOM 2 CA CYS 1 31.954 -7.042 48.762 1.00 0.00 C ATOM 3 CB CYS 1 31.233 -5.687 48.812 1.00 0.00 C ATOM 4 SG CYS 1 32.146 -4.297 49.517 1.00 0.00 S ATOM 5 C CYS 1 33.082 -6.942 47.773 1.00 0.00 C ATOM 6 O CYS 1 34.235 -6.698 48.164 1.00 0.00 O Regards, Daipayan On Tue, Nov 14, 2017 at 12:00 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Forgot to finish this one thought, sorry...
On Nov 14, 2017, at 9:47 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
An important point is that the Chimera-Modeller interface will only model one chain at a time. It does not care that other chains are there, so any added residues/loops might end up clashing with the other chains. In this case it didn’t seem
… that bad since the added residues were on the outside of the complex. However, Find Clashes/Contacts (in menu under Tools… Structure Analysis) identified a few clashes between those chains and the other chains in the merged model in my test. I only made one Modeller model of each chain. One reason you might want to try making more than one model of each chain is that they may have different numbers of clashes with the other chains in the structure. However, whether you care about this depends on what you are going to do with this overall structure. If it’s just for a picture, it’s not important, or if you were going to run minimization or dynamics, the clashes would easily resolve themselves in this case because they involve peptide termini on the outside of the complex.
Finally, if you want to use Modeller to model the multi-chain complex with awareness of the other chains, you would have to use it separately outside of Chimera.
Elaine