Pore facing residues not picked up about chap HOT 2 CLOSED

Could you provide a PDB file of the input structure you are having this problem with as well as the complete command line you use to invoke CHAP? Without a concrete example, this problem may be hard to diagnose.

Have you already tried varying the -pm-pl-margin parameter? This is the maximal distance a residue COG may have from the pore surface to be counted as pore-lining. Only pore-lining residues will be considered in the subsequent identification of pore-facing residues.

from chap.

To be honnest, I didn't remember I posted that. I solved the problem by using the pore lining residues instead of the pore facing residues when ploting the channel radius profile.
i.e., I use pf = np.array(data["residueSummary"]["poreLining"]["mean"]) > 0.5
instead of pf = np.array(data["residueSummary"]["poreFacing"]["mean"]) > 0.5

One related thing is that the N- and C-term are capped (with Amber ACE and NHE residues), which led to an error because they are not recognised. Surprisingly, I still had the error when using the -hydrophob-fallback option, not sure why. So I ended up adding those residues to the hydrophibicity scale json file. I am just mentioning this in case someone else face the same problem in the future.

from chap.