Question about Ramachandran probability assignment to attributes
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 -- *Dr. Sergio Garay* *Profesor Adjunto Càtedra de Práctica Profesional de Bioquímica* *Cátedra de Bioinformática* *Facultad de Bioquimica y Cs. BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 - Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54 (342) 4575-221 *
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 ----- 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
Thank you very much Elaine! Just to make sure I’m understanding the results correctly when assigning probabilities to each point on the Ramachandran map for my protein, could it happen that an amino acid residue like Leucine falls into a highly allowed region, but still has a low probability value for Leucines, like less than 0.0638566? If that’s the case, does it mean that the residue is in an allowed region, but the phi and psi angles are unlikely for that specific residue? Is that right? Sergio On Fri, Oct 18, 2024 at 5:51 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
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 ----- 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
-- *Dr. Sergio Garay* *Profesor Adjunto Càtedra de Práctica Profesional de Bioquímica* *Cátedra de Bioinformática* *Facultad de Bioquimica y Cs. BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 - Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54 (342) 4575-221 *
As far as I know the value assigned should be consistent with the displayed contours, **as long as you are showing the contours that apply to that class of residue** - as the help page says, "Assign Residue Probabilities assigns an attribute named ramaProb to the amino acid residues, with values taken from the appropriate dataset for each residue (Proline for prolines, etc.)," <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ramachandran/ramachandran.html>
On Oct 18, 2024, at 2:06 PM, Sergio Garay via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Thank you very much Elaine! Just to make sure I’m understanding the results correctly when assigning probabilities to each point on the Ramachandran map for my protein, could it happen that an amino acid residue like Leucine falls into a highly allowed region, but still has a low probability value for Leucines, like less than 0.0638566? If that’s the case, does it mean that the residue is in an allowed region, but the phi and psi angles are unlikely for that specific residue? Is that right?
Sergio
On Fri, Oct 18, 2024 at 5:51 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: 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 ----- 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
-- Dr. Sergio Garay Profesor Adjunto Càtedra de Práctica Profesional de Bioquímica Cátedra de Bioinformática Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
participants (2)
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Elaine Meng -
Sergio Garay