Hi Sergio,
I cannot reproduce this.  When I open 1ay7, delete chain B (leaving only chain A), show Ramachandran Plot, assign probabilities, there are no residues with probability <0.01.

Lowest probability is 0.048 for proline 29.  You have to switch to Ramachandran map for "Proline" to see the appropriate probability contour lines for prolines.

Although it looks like other residues on the plot have lower probability, it is irrelevant for all of those non-proline residues when you are showing the "Proline" contours -- each type of residue will be assigned the probability of the appropriate dataset.

I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Oct 15, 2024, at 9:40 AM, Sergio Garay via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>
> Hi everyone! I have a question regarding the use of probability assignment to attributes: for example, if I take chain A of 1ay7.pdb, open the Ramachandran plot, and ask it to assign the probabilities as an attribute, then select all residues with a probability lower than 0.01, I end up with two selected residues, one in the allowed regions for alpha helices and another in the beta sheet regions. I expected that residues outside the allowed regions or near the edges of the allowed zones would be selected, not in the center of them. Can someone explain what my mistake is? Thanks a lot!
>
> Sergio
>