hi does anyone know what all the info means`?
especially, what does the score for reference mean, and how to improve each score?
thank you for your answers-
* Clashing is related to atom distance. If atoms are too close, their electron clouds would be repelling each other, while nothing bad happens if atoms are far apart (they just don't react). Note that this applies to both the backbone and side chains-- so, if you see a segment with a bad clashing score but can't figure out why, consider showing the side chain and/or switching to a full-atom viewing mode to see what's clashing.
How to improve: Shake and/or wiggle, and rebuild if necessary.
* Packing refers to the extent that atoms are surrounded by other atoms. This is related to van der Waals interactions (see http://en.wikipedia.org/wiki/Van_der_Waals_force ).
How to improve: Manually flip large side chains or use bands to bring pieces closer together. Again, rebuild if necessary.
* Hiding is related to the hydrophobicity of the side chain. In general, orange side chains need to point inward, while blue side chains need to point outward. The general trend is roughly consistent with the size of the side chain, so you've better bury a tryptophan and leave an arginine on the outside (as a general rule-- there are exceptions).
How to improve: Manual side chain tweaks, bands, or rebuilds.
* Backbone: Refers to the configuration of backbone atoms. It is directed affected by dihedral angles (see http://en.wikipedia.org/wiki/Dihedral_angle ).
How to improve: Rebuild, in a full-atom viewing mode if higher precision is desired. Note that you may have to use bands to guide the direction of the rebuild and/or set the segment to loops to increase the range of choices for the rebuild tool.
* Side chain: The score is related to the statistical distribution of side chain configurations based on the backbone configuration. A more negative score means that the configuration is rarer in nature, and thus less likely to be correct.
How to improve: Shake and manual side chain tweaks. Rebuilding the backbone can also be considered, as sometimes you simply can't fix the side chain due to an incorrect backbone configuration.
* Reference: Apparently, it's the "reference energy" of each amino acid. This is perhaps the least intuitive part of the score function; its main use is for design puzzles as a "normalization" factor, to correct for the bias for larger side chains (which are not necessarily more stable in nature)
How to improve: You can't.
thank you for that explanation, it makes it a lot clearer and will greatly help improve the structure.
"How to improve: Rebuild, in a full-atom viewing mode if higher precision is desired."
How do you switch to "full-atom viewing mode"? Is it the "Line+H" option under "View Protein"?
The full-atom viewing mode that I use the most often is Stick+polarH. You can switch to that by pressing Ctrl+Shift+V; to switch back to normal viewing mode, press Ctrl+Shift+M. (Simply choosing Stick+polarH in the view menu would also work, but the advantage of using the hotkey is that it would also switch to element-based coloring: gray = carbon, blue = nitrogen, white = hydrogen, red = oxygen, and yellow = sulfur.)
There's a couple that have been missed: Bonding, and Disulfides. I believe Disulfides is a new one that has been added recently (bond with green and yellow stripes).
So the complete list of scoring elements would be:
Glycines don't have sidechains, so this won't appear for them.
As far as I know, any scoring elements that have a score of '0' will not appear at all.