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harryjubb / arpeggio

Calculation of interatomic interactions in molecular structures
http://biosig.unimelb.edu.au/arpeggioweb/
GNU General Public License v3.0
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Arpeggio gives "selection empty" or error for residue with no side-chain #15

Open mariaangelesjs opened 5 years ago

mariaangelesjs commented 5 years ago

Hi Harry, I am trying to select a residue with no chain (//ALA`24/CA), but when I try to calculate the interactions with arpeggio, it gives me this output:

docker run --rm -v directory-path -u XXXX:XXXX -it arpeggio python arpeggio.py /XXXX.pdb -s /0/24/ -v

INFO//12:09:16.966//Program begin. INFO//12:09:17.017//Loaded PDB structure (BioPython) INFO//12:09:17.078//Loaded PDB structure (OpenBabel) INFO//12:09:17.093//Mapped OB to BioPython atoms and vice-versa. INFO//12:09:17.250//Added hydrogens. INFO//12:09:17.480//Typed atoms. INFO//12:09:17.498//Determined atom explicit and implicit valences, bond orders, atomic numbers, formal charge and number of bound hydrogens. INFO//12:09:17.537//Initialised SIFts. INFO//12:09:17.545//Determined polypeptide residues, chain breaks, termini INFO//12:09:18.044//Percieved and stored rings. INFO//12:09:18.071//Perceived and stored amide groups. INFO//12:09:18.106//Added hydrogens to BioPython atoms. INFO//12:09:18.115//Added VdW radii. INFO//12:09:18.123//Added covalent radii. INFO//12:09:18.128//Completed NeighborSearch. INFO//12:09:18.132//Assigned rings to residues. ERROR//12:09:18.135//Selection was empty.

I've tried with -s //24/ and it gave me this:

INFO//12:10:45.387//Program begin. INFO//12:10:45.444//Loaded PDB structure (BioPython) INFO//12:10:45.504//Loaded PDB structure (OpenBabel) INFO//12:10:45.519//Mapped OB to BioPython atoms and vice-versa. INFO//12:10:45.675//Added hydrogens. INFO//12:10:45.902//Typed atoms. INFO//12:10:45.921//Determined atom explicit and implicit valences, bond orders, atomic numbers, formal charge and number of bound hydrogens. INFO//12:10:45.959//Initialised SIFts. INFO//12:10:45.968//Determined polypeptide residues, chain breaks, termini INFO//12:10:46.464//Percieved and stored rings. INFO//12:10:46.489//Perceived and stored amide groups. INFO//12:10:46.526//Added hydrogens to BioPython atoms. INFO//12:10:46.534//Added VdW radii. INFO//12:10:46.542//Added covalent radii. INFO//12:10:46.546//Completed NeighborSearch. INFO//12:10:46.551//Assigned rings to residues. ERROR//12:10:46.551//Invalid selector: //24/ Traceback (most recent call last): File "arpeggio.py", line 1406, in selection = selection_parser(args.selection, entity) File "arpeggio.py", line 187, in selection_parser raise SelectionError(original_selection) main.SelectionError

I had no issue when I was using arpeggio for a receptor with side-chains. Do you have any solution for this? Kind regards, Maria

mariaangelesjs commented 5 years ago

Hi Harry, I added the chain with a script and there was no issue. I do have to say that adding '//' does not seem to work when you don't have a chain. Kind regards, Maria

harryjubb commented 5 years ago

Hi Maria,

-s //24/ should work, and should select every residue numbered 24, so this may be a bug.

If you're able to share your PDB, please attach it to this issue, if not I can make some test data. I'll take a look when I have a chance.

mariaangelesjs commented 5 years ago

Hi Harry, I had to add a B chain for it to be recognised. Here is the link to get the pdb file https://gpcrdb.org/structure/homology_models/cnr2_human_intermediate. Even after deleting the first two lines of the pdb file, the same error appeared. Kind regards, Maria