About the selection of residues

[satyajitkhatua09]

Hi,

I have just started using the pycontact, which seems a valuable tool for different contact calculations between two segments. I am curious about the selection tabs in GUI. Do you know if I can use the residue ID despite the segid? If yes, how do I put it inside the selection tabs? I have tried with the notation as instructed in MDAnalysis. However, it fails with the error message "Probably you specified an atom selection with 0 atoms or invalid input files". I am using PSF and DCD as inputs.

Best,
Satyajit

[maxscheurer]

Hi,

probably best to try out the selection in a standalone python script first, using just plain MDAnalysis.

import MDAnalysis as mda
u = mda.Universe(path/to/topology, path/to/trajectory)

s1 = u.select_atoms("resid 1:5")
s2 = u.select_atoms("resid 10:20")

print(s1)
print(s2)

or something of the sort...

See the MDAnalysis docs also: https://docs.mdanalysis.org/stable/documentation_pages/selections.html#simple-selections

Sorry the error message is not super helpful, I'm planning to do some maintenance on PyContact in the near future...

[satyajitkhatua09]

Hi Max,

As I saw from the piece of MDAnalysis script (that you gave me), my selection was incorrect. As I have numerous segments (almost 75), I should have opted for a combination of segid and resid (like segid A and resid 1:10). Now that the selection is proper, I hope PyContact will run without an issue.

Thanks for your earnest help.

Best,
Satyajit