I am trying to use the pairwise Contact Comparison (hb/vdw/hp) for a set of different ligands bound to the same protein, taken from MD trajectories, by following the steps described in the tutorial. I generated the required files using gesamt, get_resilabels.py, get_static_contacts.py, and get_contact_singleframe.py, and successfully prepared the contact and residue label files. However, when I load these files in the Atlas module under user-defined structures and click “Add,” nothing happens (no error message and no structure is loaded). As a control, I tested the same workflow using the tutorial example dhfr_4m6l, and it loads correctly, which suggests that the Atlas module itself is functioning. This leads me to suspect a possible issue with the formatting or handling of user-defined contact/label files or with comparing multiple ligands for the same protein. I would appreciate any guidance on how to fix this issue or debug the input files.
Best
Zahra
I am trying to use the pairwise Contact Comparison (hb/vdw/hp) for a set of different ligands bound to the same protein, taken from MD trajectories, by following the steps described in the tutorial. I generated the required files using gesamt, get_resilabels.py, get_static_contacts.py, and get_contact_singleframe.py, and successfully prepared the contact and residue label files. However, when I load these files in the Atlas module under user-defined structures and click “Add,” nothing happens (no error message and no structure is loaded). As a control, I tested the same workflow using the tutorial example dhfr_4m6l, and it loads correctly, which suggests that the Atlas module itself is functioning. This leads me to suspect a possible issue with the formatting or handling of user-defined contact/label files or with comparing multiple ligands for the same protein. I would appreciate any guidance on how to fix this issue or debug the input files.
Best
Zahra