ConAn (which stands for Contact Analysis) is a tool to analyze MD trajectories through the use of contact maps and related quantities. It can be very useful for a first, exploratory analysis, i.e., identifying key contacts to be analyzed further, but can also offer alternative, possibly more precise, measures to the ones commonly used (RMSD, RMSF, etc...).
In the following few posts we will go through most of the functionalities of ConAn and its possible uses.
Hi Csaba, thank you for this lovely contact analysis tool. Could you please let me know how can I generate/plot matrix for only one side of the diagonal, i.e. one-sided off-diagonal contacts? Also is there any way to leave out (not plot) neighboring residue contacts? thanks
ReplyDeleteHi Shayon, thanks for your comment.
ReplyDelete1) Non-symmetric contacts: conan doesn't do this at the moment. I have a strong preference for symmetric matrices for the moment, as you have all the contacts formed by a residue on a single line/column instead of a part of a line then a column.
2) CONAN doesn't support this either, as the inter-residue distance matrix naturally includes "trivial contacts". And after all, whether we like it or not, residues that are close in sequence are also in contact, even if they are chemically incompatible.
Of course, once there is enough pressure from users, we'll be forced to implement these changes :) For the moment, I like the idea of a relatively uniform/recognizable output that is customizable but not to an arbitrary extent.
If I were you, I'd just change the plain-text matrices with some simple awk script, and reread them with the "REREAD" option. It's not a perfect solution, but it should be pretty easy to implement. I'm happy to help you with similar use cases.