I have been recently calculating the pore profile of a membrane protein, and I encountered an error:
chap -f closed.pdb -s closed.pdb -hydrophob-database user -hydrophob-json colour_scal.json
Standard library runtime error (possible bug):
(exception type: St13runtime_error)
Pore radius at initial probe position is infinite. Consider increasing the
maximum pore radius with -pf-max-free-dist or set an appropriate cutoff for
neighbourhood searches explicitly with -pf-cutoff.
While adjusting the cutoff distance, I noticed that it doesn't generate the appropriate radius. To verify this, I tried HOLE, and it does generate the radii. If I choose the selection(chap) of alpha carbon or side chain, it gives me truncated and large radii, approximately 20 Å. I am using the following command:
chap -f closed.pdb -s closed.pdb -hydrophob-database user -hydrophob-json colour_scal.json -pf-max-free-dist 2 # 2-100
Could you please help me identify if I am missing any steps?
Hello,
I have been recently calculating the pore profile of a membrane protein, and I encountered an error:
chap -f closed.pdb -s closed.pdb -hydrophob-database user -hydrophob-json colour_scal.json
Standard library runtime error (possible bug): (exception type: St13runtime_error) Pore radius at initial probe position is infinite. Consider increasing the maximum pore radius with -pf-max-free-dist or set an appropriate cutoff for neighbourhood searches explicitly with -pf-cutoff.
While adjusting the cutoff distance, I noticed that it doesn't generate the appropriate radius. To verify this, I tried HOLE, and it does generate the radii. If I choose the selection(chap) of alpha carbon or side chain, it gives me truncated and large radii, approximately 20 Å. I am using the following command:
chap -f closed.pdb -s closed.pdb -hydrophob-database user -hydrophob-json colour_scal.json -pf-max-free-dist 2 # 2-100
Could you please help me identify if I am missing any steps?
Regards,
Aashish