BLUE STAR STING Basic Features

STING Millennium Control Panel BASIC Commands

Here we will only describe basic commands from the STING Millennium control menu. There are 8 menu options on STING Millennium sequence window:

Clear All	HOH off
Wireframe	Ligand on
Ribbon	Ligand off
Color CPK	Ligand Pocket
Color by Chain	HOH + Ligand
Color by Structure	Charged Residues
HOH on	Hydrophobic Core

STING Millennium Control Menu and Commands

Note: Some of the commands presented here are simple copy of the standard CHIME commands. We have chosen to put them in the Action menu options for the easier access. Most usable STING Millennium commands are actual scripts, made to facilitate molecular structure and macromolecular interface analysis. We found "Interface on", "Ligand Pocket", "HOH+Interface", "HOH+ligand", Interface: 1st/2nd half and "Charged Residues" very conveniently, one stroke apart from viewing on the Graphics Window.

Clear All

This is the only way to refresh the graphics frame (if starting from scratch is desired).

Wireframe

If your graphics screen becomes too cluttered, use Clear All and then restart by using the Wireframe command. You will end up with (you guessed right!) wireframe representation of the molecule.
Note: if previously you have used "Color by chain", these color codes are retained, which we found useful once you enter into the chain of analysis procedures. If you really desire to start with original CPK colors, use option "Color CPK" in addition to "Clear All" + "Wireframe"! {Example used here is 1ppf.pdb}

Ribbon

Ribbon simply turns on ribbon around protein main chain backbone. {Example used here is 1ppf.pdb}

Color CPK

This option is made available for the single purpose of convenience: easy, one stroke action to obtain, for example, Interface built in earlier analysis, color coded CPK (instead of color coded with respect to chain identifier, e.g.)! {Example used here is 1ppf.pdb}

Color by Chain

Convenient coloring by Chain also gives you opportunity to see if any chain is actually broken by introduction of the gap in the sequence (this info, however, could be easily observed by looking at the Sequence Window.) {Example used here is 1ppf.pdb}

Color by Structure

This command colors the molecule by protein secondary structure. Alpha helices are colored magenta, [240,0,128], beta sheets are colored yellow, [255,255,0], turns are colored pale blue, [96,128,255] and all other residues are colored white. The secondary structure is either read from the PDB file (HELIX and SHEET records), if available, or determined using Kabsch and Sander's DSSP algorithm.
Note:regions of protein fold colored by this command DO NOT NECESSARILY coincide with Secondary Structure identifiers (red and blue lines within the Sequence Window). Difference originates in calculated versus indicated nature of two approaches, respectively. This is very nicely compared by Protein Dossier presentation.{Example used here is 1ppf.pdb}

HOH on

STING Millennium default Graphics Window, comes with crystal waters turned on. If present, these water molecules might make further analysis difficult, as they might clog the picture. In this case, use command "HOH off". Later in an analysis, one might wish to turn them on, for examination of their presence within interface layer, for example. Once you use "HOH on" button, water molecules will change from default red color to magenta! This is done in order to facilitate visual identification of HOH molecules, especially in cases when default HOH color, red, is also used by other chain or ligand!

HOH off

STING Millennium default Graphics Window, comes with crystal waters turned on. If present in large number, waters should be removed from the visual using this command!

Ligand on

This command will turn visual presentation of any present ligands on.
If you do not see single atom HETATOMs such as Cu, Mg, Mn, Zn, Fe, Cl, Ca, Br etc., see here how to proceed!

Ligand off

Somewhat surprisingly, this command, really turns ligand visual off. :)

Ligand Pocket

"Ligand Pocket" will erase anything else from the graphics frame but ligand and residues side_chain atoms in contact with it! Contact is defined by distance, set to 4.0 Angstrom, and measured between ligand atoms and any other atoms belonging to ligand surrounding chains! This feature is very convenient, once you turn on the wireframe display of the rest of the molecule, by using "Wireframe" command. Position of the Ligand and surrounding molecules will be very clearly displayed for further analysis. Combine this with Ligand on/off, Color by chain and get better insight into ligand 3D environment! Also, very much used in combination with HOH + Ligand!
Note: distance of 4.0 Angstroms will pretty much satisfy requirements for both hydrogen bond formation, as well as for hydrophobic interactions!
Note #2: there is a TUTORIAL with worked example for this usuful STING option!
If you see number of residues being indicated as a POCKET, but no LIGAND to which they are associated, this does not necessarily means that STING made a mistake. It only reflects limitation of the script we used to paint multi-atom LIGANDS and not single atom ones. See here how to proceed.

HOH + Ligand

This command will have visualized Ligand and water molecules in contact with it. It is often necessary to have this information on contacting water molecules around the ligand for proper H-bond counting. Some structural water molecules are identified easily in this way!
Contact between ligand and HOH molecules is defined here by distance, set to 3.3 Angstroms, and measured between ligand atoms and any other HOH molecule (actually, in most cases, an Oxygen atom).
Note: distance of 3.3 Angstroms is considered maximum distance between Hydrogen donor and acceptor, that could still bring about hydrogen bond formation.

Charged Residues

This command will visualize all charged residues using van der Waals dotted surface. All lysines and arginines will be blue color coded, aspartic acid and glutamic acid will be red and histidine will be color coded cyan. This is a very useful feature, once you would like to know charge distribution in vicinity of ligand or maybe at molecular interface!
Note: this command will visualize (turn on) all charged residues, irrespective to the chain identifier. We found this convenient in most cases, as user can get CPK presentation of charged residues in the chain of interest, and dot color-code of charge residues in contact with interface in focus (and not belonging to the same chain) - therefore having glimpse of complementarity)! {Example used here is 1ppf.pdb}

Hydrophobic Core

This command will visualize all hydrophobic residues (supposedly located in the core of the protein) in CPK presentation and also all charged residues using van der Waals dotted surface. {Example used here is 1ppf.pdb}

Windows & Int Surface Menu Options:

Interface on
Interface HOH on
Interface Component : View 1st Half
Interface Component: View 2nd Half
1st half HOH
2nd half HOH

Interface on

Obviously, this command only functions for the pdb files with more than one chain. For the list of all files with more than one chain, the user can consult our PDB_Mining. To generate image bellow, we used 1ppf.pdb. In green thick wireframe is the interface part (1st half) that belongs to the E chain and in thick cyan wireframe is the interface part that belongs to the I chain. {Example used here is 1ppf.pdb}

This is one of the most used commands in STING Millennium . What we like about it is the simplicity of getting general information on interfaces between two molecular chains, all in one mouse stroke. This command will turn on only atoms at an INTERFACE of the first two chains in a PDB file. The choice of chains for which user desires to see Interface, is the essential for proper interface building for all pdb files with more than 2 chains.. In combination with command "Color by chain" (issued prior to Interface on) graphical information is even more emphasized.
Note:Interface is defined based on a distance, set to 8.0 Angstroms, and measured between any two atoms in different chains! A value of 8.0 Angstroms was chosen empirically; we first tried a distance of two times 3.3 Angstroms (Hydrogen acceptor from one chain, to water molecule, to hydrogen donor on the other chain). This would be distance of 6.6 Angstroms, but we found that graphical presentation of the interfaces is much more "complete" if distance of 8.0 Angstroms is used. We judged completeness by how well an interface is populated by atoms, or how many holes we have on the chains interface.
Obviously, the user should consider Interface graphics presentation more as a guide, than as a exact interface definition.