Hello, You misunderstand "rainbow" ("color seq"). It doesn't go by the order of residues you give in the command. It colors residues in their sequential order along the biopolymer chain, for example N-term -> C-term for a peptide.
To give four colors to those four residue types, you would need to give four different simple coloring commands. You can put those four commands together to define an alias or a custom preset, however, and then (after the alias or preset is defined) execute that alias or preset with a single command.
alias https://rbvi.ucsf.edu/chimerax/docs/user/commands/alias.html
custom preset https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup
The laborious way to get the transparency you want at each frame has already been explained in many previous posts responding to your questions.
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 Apr 24, 2024, at 2:31 AM, Enrico Martinez jmsstarlight@gmail.com wrote:
Thank you very much Elaine !
Actually by the automatic coloring of the nucleotides, I mean something like
color seq :DT*,DG*,DC*,DA* target f palette blue:red:gold
but apparently it does not work for nucleotides compared to simple coloring
color :DT*,DG*,DC*,DA* blue target f
One more question (I had already asked about this in the multimeric protein). In fact I would like to set different levels of the transparency for protein and DNA in the MD trajectory:
# general transparence options transparency #1 80 # Make surface DNA more transparent then the DNA surface gridSpacing 0.4 # set surface style for protein rainbow protein target s palette Paired-12 transparency 10 # set surface style for DNA rainbow :DT*,DG*,DC*,DA* target s palette Oranges transparency 90
Apparently, this does not work for the DNA-protein complex either, because in the first snapshot everything looks fine, but then when I play the trajectory, both selections become equally transparent.
Yours sincerely
Enrico
Il giorno mar 23 apr 2024 alle ore 18:06 Elaine Meng meng@cgl.ucsf.edu ha scritto: I don't know exactly what is in your structure, but you can use "color" with "target f" to color nucleotide representations whatever color you want. You can give residue number(s) to color the stubs or other nucleotide representations (tube, slab, etc.) of only specific residue(s).
See "simple coloring" commands: https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple
The default "bynucleotide" coloring uses standard residue names. See "coloring by residue type": https://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html#residue
You could either change the names of those residues to standard names, or you can just color them manually, i.e. with individual commands as mentioned above, or even add your own custom preset that includes whatever nonstandard names that tleap produces.
For this question seems like it would be easier to just try it yourself than to wait for an answer, but I'll try to answer below:
Would it be possible to change the style of all the residues e.g. showing them ass ring fills or like a color bricks (default vizualisation which looks very cool!) using selection expressions like :DT*,DG*,DC*,DA* ?
Yes, you can use * in residue names as mentioned here https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#wildcards
...and change style using "nucleotides" command https://rbvi.ucsf.edu/chimerax/docs/user/commands/nucleotides.html
However, if you want to change ALL of the nucleotide residues, it seems like you don't need to specify any residues, just do the whole structure, e.g.
open 1bna nuc fill
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 Apr 23, 2024, at 8:14 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
P.S. I could partially fix the issue using the following command which reset the view. nucleotides ladder radius 0.4 showStubs true
However, the first two sugar pairs are colored in grey compared to others (see another picture attached). Is it possible to change the color representation for the selected residues or alternatively implement some palettes presets for all of them at once ?
Yours with thanks
Enrico
Il giorno mar 23 apr 2024 alle ore 12:01 Enrico Martinez jmsstarlight@gmail.com ha scritto: Dear Chimera-X users,
I have a question about the visualisation of the DNA structure obtained after tleap processing for Amber. As I have noticed, due to the renaming of the DNA residues, some of the sugar parts are not correctly recognised by Chimera-X (see the attached screenshot) and so these elements are only displayed as organic ligands. Would it be possible to change its style using some commands, assuming that the names of the residues located at the terminal parts of the DNA helix are DC5, DG3 and DT5, DT3 (so that Amber adds numbers to them)?
Would it be possible to change the style of all the residues e.g. showing them ass ring fills or like a color bricks (default vizualisation which looks very cool!) using selection expressions like :DT*,DG*,DC*,DA* ?
Many thanks in advance !
Enrico <test2.png>