Hello, I'm evaluating changes in crystal packing between different forms of my protein. I use NCONT to calculate the number of atoms within a distance of 10 A from each CA atom of the protein chain. My protein is also a crystallographic dimer, then I want to list contacts between the two monomers in the ASU too. When I run the calculation for chain A, using the option "all interchain contacts" in NCONT GUI, I obtain the desired output: contacts between A and symmetry related A or B chains, plus contacts between A and B in the same ASU. The problem appears when I repeat the calculation for chain B: contacts between symmetry related molecules are listed, but the contacts between chain A and B in the ASU are replaced by the intramolecular ones. I copy below the header of log files generated by NCONT. I can obtain the desired output by calculating all the contacts (using the +/- two unit cells in NCONT), and removing the intramolecular ones later but...What is the explanation for the different behavior when I run the same calculation using the A or B chains?
Thanks log for chain B: Input cards Data line--- source "B/1-104/CA" Data line--- target "B, A/1-104/[C, O, N, S]" Data line--- mindist 0.0 Data line--- maxdist 10.0 Data line--- cells INTER Data line--- symm P21 log for chain A: Data line--- source "A/1-104/CA" Data line--- target "B, A/1-104/[C, O, N, S]" Data line--- mindist 0.0 Data line--- maxdist 10.0 Data line--- cells INTER Data line--- symm P21
