Restraints Editor Exclusively Ligands (REEL)
- Author
- Purpose
- Screen Shots
- General Procedure
- Input
- Editing
- Examples
Restraints Editor Exclusively Ligands (REEL)
Author
Nigel W. Moriarty
Purpose
Edit the geometry restraints of a ligand using a Graphical User
Interface (GUI) including a 3D view of the ligand and a tabular view
of the restraints.
Screen Shots
General Procedure
The general procedure is to load a restraints file (CIF) and
manipulate the restraints via the table or molecule view. The
geometry of the revised restraints can be tested using the
File->Guesstimate option. The final restraints can be saved to a CIF
file for use with phenix.refine. The corresponding PDB file can also
be saved.
Input
Restraints can be loaded into REEL using the command line, the
pull-down menu to open a file and a pull-down menu to run
eLBOW. Restraints files from eLBOW contain both the restraints and
cartesian coordinates. For the purposes of REEL, the coordinates are
generated by the restraints and can not be edited directly. The
background colour is light steel blue to show that it is not used in
the geometry editing actions.
REEL can load a molecule geometry from any format the eLBOW can read,
including PDB, Mol2D and SDF. If the file does not contain the
bonding information, the bonding is automatically determined using
proximity. The limit on the size of molecule that the bonding is
automatically determined is set at 200 atoms.
Molecule up to 2000 atoms can be loaded using the --view but only the
bond connectivity is determined. The bond order is set to one but can
be changed interactively.
Molecules can be loaded into REEL using the --reel option for eLBOW or using
the eLBOW GUI dialog available in REEL.
Editing
The geometry restraints (bonds, angles, dihedrals, planes and chirals)
are the driving coordinates in this editor. The cartesian coordinates are
displayed in the atoms table only because there are generated for the
viewer display. They are the driven coordinates and are therefore ignored
if changed in the editor.
Many cells in the table view of the restraints can be changed but care must
be taken to ensure that the changes are local or global. For example, changing
an atom name in the bonds table view will only change it in that row. If you
wish to change the name of the atom in all the restraints for should use the
right mouse menu in the viewer window or change it in the atoms table view.
The colour of the cell gives the impression as to whether the changes are
propagated elsewhere. The cells, in some cases, have not been made read only
to allow the user to make changes as desired.
Clicking an atom in the molecule view will highlight the various
related topological elements in the table view and vice versa. Use
the checkbox in the table view to remove a restraint from optimisation
and output file. Chiral centres can be changed in the table view.
Examples
To load a previously created restraints file
phenix.reel atp.cif
To load a restraints file into REEL from eLBOW
phenix.elbow --smiles O --reel
To load all the unknown ligands from a PDB file
phenix.reel model.pdb --do-all
or a single residue
phenix.reel model.pdb --residue ATP
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