yasara.request	The request string sent by YASARA to the plugin
yasara.opsys	The current operating system, "Linux", "MacOS" or "Windows"
yasara.version	The YASARA version string X.Y.Z
yasara.serialnumber	YASARA's serial number
yasara.stage	The YASARA stage View, Model, Dynamics or Structure
yasara.plugin.name	The name of the plugin (e.g. ftppdb.py)
yasara.plugin.config	A Python dictionary with the options from the plugin config file *.cnf
yasara.plugin.exitcode	The exit code returned to YASARA when the plugin ends
yasara.owner.firstname	Your first name
yasara.owner.email	Your e-mail address
yasara.selection	A list of selections with one entry for every selection menu you defined
yasara.selection[i].objects	The number of objects selected in the ith selection menu
yasara.selection[i].object[j]	The obj_descriptor (see below) for the jth selected object in the ith selection menu
yasara.selection[i].molecules	The number of molecules selected in the ith selection menu
yasara.selection[i].molecule[j]	The mol_descriptor (see below) for the jth selected molecule in the ith selection menu
yasara.selection[i].residues	The number of residues selected in the ith selection menu
yasara.selection[i].residue[j]	The res_descriptor (see below) for the jth selected residue in the ith selection menu
yasara.selection[i].atoms	The number of atoms selected in the ith selection menu
yasara.selection[i].atom[j]	The atom_descriptor (see below) for the jth selected atom in the ith selection menu
yasara.selection[i].texts	The number of text input boxes in the ith selection menu
yasara.selection[i].text[j]	The text typed into the jth text input box in the ith selection menu
yasara.selection[i].numbers	The number of number input boxes in the ith selection menu
yasara.selection[i].number[j]	The number typed into the jth number input box in the ith selection menu
yasara.selection[i].checkboxes	The number of checkboxes in the ith selection menu
yasara.selection[i].checkbox[j]	The state of the jth checkbox in the ith selection menu (1=hooked, 0=not hooked)
yasara.selection[i].switchbox	The number of the hooked switchbox in the ith selection menu, None if there was no switchbox
yasara.selection[i].listentries	The number of selected list entries in the ith selection menu
yasara.selection[i].listentry[j]	The jth selected list entry in the ith selection menu
yasara.selection[i].filenames	The number of selected filenames in the ith selection menu
yasara.selection[i].filename[j]	The jth selected filename in the ith selection menu

°  Object descriptors identify selected objects Object descriptors are instances of the class obj_descriptor. Typically, you loop over all object descriptors in the ith selection menu: for j in range(yasara.selection[i].objects): object=yasara.selection[i].object[j] And then access various object properties: object.name The name of the object object.number.inyas The unique number/ID of the object in YASARA (a string, starting with 1) object.number.inall The sequential number of the object in the soup (a string, starting with 1) You could then color the object red: yasara.ColorObj(object.number.inyas+",Red") °  Molecule descriptors identify selected molecules Molecule descriptors are instances of the class mol_descriptor. Typically, you loop over all molecule descriptors in the ith selection menu: for j in range(yasara.selection[i].molecules): molecule=yasara.selection[i].molecule[j] And then access various molecule properties: molecule.name The name of the molecule (that's the chain name in the PDB file) molecule.number.inyas The unique number/ID of the molecule in YASARA (a string) molecule.number.inall The sequential number of the molecule in the soup (a string, starting with 1) molecule.number.inobj The sequential number of the molecule in the object (a string, starting with 1) molecule.object The object descriptor for the object the molecule belongs to You could then display the molecule as sticks: yasara.StickMol(molecule.number.inyas) Or delete the entire object containing this molecule: yasara.DelObj(molecule.object.number.inyas) °  Residue descriptors identify selected residues Residue descriptors are instances of the class res_descriptor. Typically, you loop over all residue descriptors in the ith selection menu: for j in range(yasara.selection[i].residues): residue=yasara.selection[i].residue[j] And then access various residue properties: residue.name3 The name of the residue in three letter code. residue.name1 The name of the residue in one letter code. residue.number.inyas The unique number/ID of the residue in YASARA (a string). residue.number.inall The sequential number of the residue in the soup (a string, starting with 1). residue.number.inobj The sequential number of the residue in the object (a string, starting with 1). residue.number.inmol The sequential number of the residue in the molecule (a string, starting with 1). residue.number.inpdb The number of the residue in the PDB file (a string, last character may be the insertion code). residue.object The object descriptor for the object the residue belongs to. residue.molecule The molecule descriptor for the molecule the residue belongs to. You could then color the residue yellow: yasara.ColorRes(residue.number.inyas+",Yellow") Or display a ribbon for the entire molecule containing this residue: yasara.ShowSecMol(residue.molecule.number.inyas,"Ribbon") If you wonder why a '+' is used to combine the arguments in the first case, while a comma ',' is used in the second case, look here . °  Atom descriptors identify selected atoms Atom descriptors are instances of the class atom_descriptor. Typically, you loop over all atom descriptors in the ith selection menu: for j in range(yasara.selection[i].atoms): atom=yasara.selection[i].atom[j] And then access various atom properties: atom.name The name of the atom atom.namespaced The name of the atom including spaces (always four characters) atom.altloc The alternate location indicator of the atom atom.position The position of the atom, a list with three cartesian coordinates atom.occupancy The occupancy field of the atom in the original PDB file atom.bfactor The B-factor of the atom atom.number.inyas The unique number/ID of the atom in YASARA (a string). atom.number.inall The sequential number of the atom in the soup (a string, starting with 1, the same as .inyas). atom.number.inobj The sequential number of the atom in the object (a string, starting with 1, usually the same number as in the PDB file). atom.number.inmol The sequential number of the atom in the molecule (a string, starting with 1). atom.number.inres The sequential number of the atom in the residue (a string, starting with 1). atom.object The object descriptor for the object the atom belongs to. atom.molecule The molecule descriptor for the molecule the atom belongs to. atom.residue The residue descriptor for the residue the atom belongs to. You could then color the atom green: yasara.ColorAtom(atom.number.inyas+",Green") Or delete the entire residue the atom belongs to: yasara.DelRes(atom.residue.number.inyas)