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Recipe: Atom Explorer v1.0
Created by LociOiling 2 2
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Name: Atom Explorer v1.0
ID: 102531
Created on: Tue, 11/07/2017 - 03:03
Updated on: Tue, 11/07/2017 - 03:03

Use spacebands to identify the atoms of a ligand or a regular segment. Save the user's picks, output them in Lua table format for recipe use.

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LociOiling's picture
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Joined: 12/27/2012
Groups: Beta Folders
bands to identify atoms in a ligand (or a regular segment)

Several recent puzzles have involved mystery ligands, small molecules floating in space somewhere near the protein. Unlike the familiar 20 amino acids, the exact makeup of these ligands can be hard to determine.

Atom Explorer draws spacebands to each atom of a specified segment. By default, it starts with the last ligand segment in a puzzle, but you can point it to any segment if desired.

The recipe prompts for chemical element of each atom. Using one of the "CPK" coloring options helps to identify the elements.

For nitrogen and oxygen, the recipe also prompts for whether the atom is a hydrogen bond donor, acceptor, or both. Normally nitrogen is a donor, and oxygen can be either an acceptor, or a donor/acceptor.

The recipe records the user picks, and, at the end, outputs them to the scriptlog in table format. The table can be imported into another recipe.

setup and view options

Some puzzles, like 1446, may allow you to draw the ligand away from the protein. If so, use the move tool to get some space between the ligand and the protein.

Otherwise, the "X-ray tunnel for ligand" view option may help you to see what's going on. You can drag on the black border of the tunnel to make it wider or narrower. Fading the background (via control-shift-drag on background) or the foreground (via control-alt-drag on background) may also help.

For a ligand puzzle, the "Ligand Specific" color option and the "Cartoon Ligand" view protein option probably produce the best results.

Otherwise, be sure to use "EnzDes" coloring or one of the "CPK" options.

These options put a blue sleeve around nitrogen atoms, a red sleeve around oxygen atoms, a white sleeve around hydrogens, and a yellow sleeve around sulfurs. Carbons have a light blue-gray color, the same color as the bonds between atoms. Metals like zinc or calcium have an indistinct light color, such as a kind of light green for calcium.

In addition to the CPK sleeve colors, the appropriate "show bonds" option and "show bondable atoms" highlight whether an atom is a hydrogen donor, acceptor, or both an acceptor and a donor.

For example, with a ligand, use "show bonds (non-protein)" and "show bondable atoms" to highlight the bondable atoms. Usually, nitrogen is a donor. Oxygen can be an acceptor, but it can also be a donor/acceptor if it's bonded to a hydrogen atom.

Running the recipe

Once you have the correct view options set and the ligand or segment is visible, run the recipe. The recipe selects the last segment to analyze by default. The segment selected and the range of atom numbers to look at can be changed in the first dialog.

Once the segment number is confirmed, the recipe starts by drawing a heavy band from the first atom specified to a point in space. The free end of the band can be moved around to help clarify which atom the band is attached to. The recipe prompts for the element of the atom, which can be identified by the CPK colors described above. A comment about the atom can also be entered.

For nitrogen and oxygen, the recipe prompts for donor/acceptor/both. These can be identified by the spheres drawn when "show bonds" and "show bondable atoms" are selected.

The atoms analyzed are written to the scriptlog in Lua table format. The resulting table can be used in another Lua script.

The scriptlog output also includes an approximate chemical formula and a count of hydrogen bond donors, acceptors, and donor/acceptors.

heavy versus light

Foldit follows the convention that all "light" atoms (hydrogens) appear after the other "heavy" atoms. Once you identify the first hydrogen, all the remaining atoms should be hydrogen. The recipe offers to identify all the remaining atoms as hydrogen, which can speed things up considerably. The default atom choice also becomes hydrogen instead of carbon after the first hydrogen.

The recipe reports the heavy and light atom ranges to the scriptlog.

regular amino acids

The recipe can also be used with the amino acid segments (residues) that make up a protein.

Using a "cartoon" view option, you won't be able to see the backbone atoms of an amino acid residue. Use "line+H" or "line+polarH" to help reveal these atoms.

The atom numbers for the first and last amino acid residue in a protein differ slightly from the ones in the middle. The first segment (or "N terminal") has an extra hydrogen, but that's not usually a concern.

The last segment (or "C terminal") has an extra -OH group. The O from the -OH group is counted before any of the sidechain atoms. As a result, the sidechain atoms of the last segment of a protein are all numbered one higher than the sidechain atoms of the same AA residue in the middle of the protein. When banding to a specific atom, recipes need to account for this difference in the last atom.

The nice part about the usual 20 amino acids is that they're always the same, aside from the quirks of atom numbering, so you don't absolutely need this recipe to identify the atoms.

metal atoms

Metals like zinc and calcium are hard to identify by color. So far, it's easiest for figure them out by examining certain Foldit configuration files, which use poorly documented formats associated with the underlying Rosetta software.

Atom Explorer just has a "metal" pick for element, and puts "mx" in the element column of the output table.

table output

The recipe outputs a table called AtomChart in Lua source format. The table can be copied into another recipe for use in banding.

The table has five columns:

  • segment number
  • atom number
  • chemical element (as identified by the user)
  • hydrogen bonding (user-pick, blank or D for donor, A for acceptor, and B for donor/acceptor)
  • optional user comment
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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Microsoft, Adobe, RosettaCommons