Thank you so much for the response. Defining values and corresponding colors with a custom script works to modify the .pb file. Thank you! Best wishes, Hannes
On Feb 26, 2025, at 7:49 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Hannes, The problem may be that there is no tool or command to color pseudobonds by pseudobond attribute values. I can create the pseudobonds en masse with a .pb file and assign them pseudobond attributes by specifying the endpoint atoms in a .defattr file (which doesn't require them to be in separate models), but get stuck at the coloring stage.
Example, with input files attached to this message to create a few attributes assigned integer values for attribute "pbints": open 1zik show atoms hide ribbons open test2.pb open test2.defattr
We also briefly entertained the idea of making each on a separate model as you describe, then assigning model attributes, then coloring by model attribute. However, that also does not work, because it's only enabled for atomic models, not pseudobond models.
The only approach I can think of is to develop your own code to map values to colors and then put the colors directly into the .pb file. <https://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>
Somehow the value->color mapping is done under the hood for "alphafold contacts" but I can't say more about whether it could be adapted to your purposes easily -- maybe the developer(s) can comment further on that? <https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts>
Sorry for the difficulties, 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
<test2.pb><test2.defattr>
On Feb 26, 2025, at 3:55 PM, hannes.ludewig--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear developers,
I am trying to color pseudobonds by an individual (per-bond) attribute value (integer). I seem to be unable to use .pb files to create individual pseudobonds. And when I am using the pbond command several times providing an individual name for each pseudobond thus creating individual models (#1.1, #1.2, etc) I am unable to assign an attribute and color all pseudobonds according to the corresponding attribute value. What I want to create is similar to the alphafold contacts colored by PAE. Only that the values I am providing aren't PAE and I would like to determine the residue pairs that form each pseudobond. I apologize in case I am overlooking something obvious, but your help and/or clarification would be very much appreciated. Thank you.
Best wishes, Hannes