Chirality Plugin, Version 1.4
The Chirality plugin allows the user to:
- Detect cis chirality errors in protein and nucleic acid structures.
- Visualize chirality errors.
- Correct chirality errors.
- Define harmonic restraints to enforce chirality in simulations with NAMD.
See also the Cispeptide plugin to detect, visualize, correct, and enforce peptide bond configuration in protein structures.
Tutorial: A tutorial describing both the Chirality and the Cispeptide plugins can be found here.
Please cite the following reference in any work that uses the Chirality plugin:
Graphical interface
The graphical interface of the Chirality plugin is described in this tutorial.
Command-line interface
To load the plugin, type in the VMD text console or the Tk Console: package require chirality. The chirality commands should then be available. Simply typing chirality prints a list of available commands:
Usage: chirality
Commands:
check -- identify chirality errors
list -- list identified chirality errors
minimize -- fix chirality errors using energy minimization
move -- move hydrogen atom to fix chirality
reset -- reinitialize plugin state
restrain -- generate NAMD extrabonds file to prevent chirality changes
show -- visualize identified chirality errors
Under the hood
Detection of chirality errors
Supported chiral centers. The following table lists all chiral centers supported by the Chirality plugin. For each set of residues, each chiral center is defined by a set of atom names (enclosed in curly braces). The order of the last four atoms in each set (heavy atoms) was chosen so that the improper dihedral angle between them is negative if the chirality is incorrect. The first atom corresponds to the hydrogen atom to be moved in order to correct the chirality. When multiple atom names corresponding to the hydrogen atom are supported, the list is enclosed by curly braces.
| Residue names | Atom names |
|---|---|
| A G ADE ADN GUA RA RG DA DG RA3 RG3 RA5 RG5 ATP ADP AMP GTP GDP GMP 1MG 2MA 2MG 6MA 7MG DMA MA6 MRG OMG SPA MIA | {H1' C1' C2' N9 O4'} |
| C U CYT URA RC DC RU T DT RC3 RU3 RC5 RU5 3AU 3MU 4SU 5MC 5MU DHU M4C MRC OMC MRU OMU RCP | {H1' C1' C2' N1 O4'} |
| PSU 3MP | {H1' C1' C2' C5 O4'} |
| ADE ADN A RA DA RA3 RA5 CYT C RC DC RC3 RC5 RCP GUA G RG DG RG3 RG5 URA U RU T DT RU3 RU5 GTP GDP GMP ATP ADP AMP | {H3' C3' C4' C2' O3'} {H4' C4' C5' C3' O4'} {{H2'1 H2' H2''} C2' C3' C1' O2'} |
| CH 1MG 2MA 2MG 3AU 3MP 3MU 4SU 5MC 5MU 6MA 7MG DHU H2U DMA MA6 M4C MRC OMC MRG OMG MRU OMU PSU SPA MIA | {H2' C2' C3' C1' O2'} |
| 3AU | {H24 C12 N40 C13 C11} |
| ALA ARG ASN ASP CYM CYS GLN GLU HSP HSE HSD HIP HIE HID HIS ILE LEU LYS MET PHE PRO SER THR TRP TYR VAL | {HA CA N C CB} |
| THR | {HB CB CA OG1 CG2} |
| ILE | {HB CB CA CG1 CG2} |
Missing atoms. Supported chiral centers are listed above. If any atom used in the definition of the chiral center is missing in the input structure, the corresponding chiral center is ignored in the analysis.
Alternative conformations. PDB files can contain alternative conformations for certain atoms (altLoc field). In such cases, the Chirality plugin considers only the first conformation.
Correcting chirality errors
Moving a hydrogen atom. For each chirality error to be corrected, the hydrogen atom is moved in order to flip the chirality configuration. The Chirality plugin moves the corresponding hydrogen atom in the direction of its covalent bond by a distance equal to two times the original bond length. If this operation results in atoms being within 0.5 Angstroms of each other, the hydrogen atom is moved progressively back until the clashes are resolved and a warning message is printed.
Minimizing/equilibrating the modified structure. After hydrogen atoms for selected chiral centers were moved, the user can minimize (and optionally equilibrate) the structure using AutoIMD (see above). The Chirality plugin provides the AutoIMD plugin with a subset of the original structure containing a region within 10 Angstroms of the modified chiral centers. In addition, the Chirality plugin communicates with the AutoIMD plugin, generating a list of harmonic restraints that are then applied to improper angles corresponding to the modified chiral centers in order to enforce the correct chirality during energy minimization and/or equilibration.
