lafita / tadoss Goto Github PK

We are currently using the sequential index of the residue in the structure but this might generate problems with structures with missing residues (although method should not work on those) and makes the mapping and visualization harder.

Try to use/display the residue numbers from the PDB file.

For convention to the contact matrices.

• Do not show the number 0 in contact matrix plot, matrix should start at 1
• Show diagonal identity line
• Show some of the panel grid lines to orient viewer better

Parameters for the alchemical free energy are not available from the bundle script, including the length of the linker and the hinge loop.

The current implementation only removes terminal residues without a single contact, but this is clearly insufficient for most cases where the boundaries of the domain are extended and causes the dGjoin to be very instable and has a lot of influence on the final estimation.

Removing any additional terminal residues in the domain is necessary to produce comparable results and make the method fully automated so it does not depend so much on how the domain boundaries where chosen.

Currently missing residues cause the calculation to fail (very first stage).
Detect missing residues in the input structure and do something to handle it.