The ISOLDE menu

When you start ISOLDE, a new “ISOLDE” entry will appear in the main ChimeraX menu. This provides access to various small, occasionally-used functions.

Model Building

  • Add Hydrogen: add a single hydrogen in a chemically-sensible position to the currently selected atom, if supported by its chemical state. If addition of another hydrogen is not chemically sensible it will not be placed.

  • Add Oxt: add an OXT atom to a C-terminal amino acid residue to form the carboxylic acid. In general this should only be done for true C-terminal residues, unless you are certain that this is a proteolytic cleavage site.

  • Make Bond: create a bond between two selected atoms. Use with care: this method does not check for chemical sensibility, nor delete hydrogens.

  • Merge Models Into Working Model: takes all models with at least one atom selected and merges copies of them into ISOLDE’s current working model. Chains in the added models will be renamed as necessary to avoid conflicts.

  • Protonate Acid Sidechain: if a Glu or Asp residue is selected, adds a hydrogen to one of its acid oxygens.

  • Remove All Altlocs: delete all alternate conformers in the model, setting the occupancies for the remaining active altloc atoms to 1.0.

  • Remove Bond: delete a bond between two selected atoms. As for Make Bond, this does not make any other modifications to the model such as addition/ removal of hydrogens.

Disulphides

  • Break Disulphide: break the disulphide bond between two selected cysteine residues, adding hydrogens if hydrogens are present in the rest of the model

  • Create Disulphide: create a disulphide bond between two selected residues

  • Make All Sensible Disulphides: find and bond all pairs of cysteine residues in your model whose sulphur atoms are within 3 Angstroms of each other but not bonded. If three or more cysteine residues are clustered in an ambiguous manner, they will not be bonded and a warning message with their identities will be printed to the log. (NOTE: this will only be effective if used before running simulations - afterwards, the sulphur atoms will be pushed too far apart to be recognised as potential disulphides)

Prep

  • Convert Amber Files: (Deprecated for most purposes - for most common ligands, use ISOLDE’s Residue Parameterisation widget). Looks in the current working directory for pairs of files named ({name}.frcmod, {name}.mol2) (i.e. generated by AMBER’s ANTECHAMBER for a new ligand), and converts each pair into the OpenMM ffXML format required by ISOLDE. Use ISOLDE’s “Load residue MD definition(s)” button to allow simulation of these residues.

    NOTE: this tool requires ParmEd, which is not currently part of the ChimeraX distribution. If you don’t have it, you will be given the choice to automatically install it. Installation of ParmEd requires the availability of a compiler on your system path - for Linux this is generally no problem, but in MacOS you will need to have XCode installed while in Windows you will need a recent Visual Studio installation.

NOTE: the following two tools require Phenix and ParmEd. Phenix must have the $PHENIX environment variable set (e.g. by running “source phenix_env.sh” prior to starting ChimeraX)

  • Convert pLDDT to B-factors: models predicted by AlphaFold2 and its variants fill the B-factor column with predicted Local Distance Difference Test (pLDDT) values, which have an inverse relationship to B-factors. Use this to convert these to estimated B-factors in ISOLDE’s current model.