Make hydrophobic interactions visible

Started by Susume

tamirh Lv 1

This is the visualization that should cover this now:

View Options -> Show expected residue burials

tokens Lv 1

Can you say a bit more about what this viewing option actually shows? I can't really guess the logic from turning the viewing option on.

Susume Lv 1

Thank you for working on this issue. I'm having trouble understanding the new visualization. It seems to highlight most of the sidechains on the outside of the protein, some in red and some in white. It is not clear to me what it means.

I was hoping for sidechains with positive "hydrophobic interactions" to be marked in some way (and sidechains lacking these interactions to remain unmarked). In a normal puzzle I expect these would be on the inside of the protein, not the outside. On a design puzzle or symmetry puzzle they might be in the space between the proteins. In the other feedback, I was hoping the buried hydrophilics on the inside of the protein could be marked to make them more visible. The added highlighting on the outside of the protein currently makes the buried ones a bit harder to find. I wonder if the new visualization can be tweaked in some way to make it concentrate on sidechains inside the protein, making the two groups I mentioned easier to see.

I also wonder if others are finding the new highlighting helpful, or have suggestions for making it more helpful.

tamirh Lv 1

What it is doing right now is looking at some of the score terms of each residue and comparing the result with data from a large set of native structures. The score terms from the native structures give a range of values.

The red coloring shows where your residues are doing much worse than amino acids of the same type when compared to the native structures. The white coloring shows where your residues doing well. The intensity of the color shows you how well or how poorly the residue is doing.

Yes, the visualization can get pretty cluttered when the puzzle is large. I added both the hydrophobic and hydrophillic residues because I thought it might be useful (the score terms were not specific to hydrophobics).

I will definitely be changing the visualization, so any comments about how you think it would be better it would help.