Hi Elaine,
thank you for the information, that is very helpful.
Mau
*Mauricio Losilla, PhD* Integrative Biology; and Ecology, Evolution, & Behavior Michigan State University he, him, his
On Tue, Apr 5, 2022 at 10:28 AM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Mauricio, You definitely can show specific model(s) like spaghetti or licorice without changing their secondary structure assignments -- just make the width and cross-section of all protein cartoon the same with "cartoon style". E.g. like menu: Presets... Licorice/Ovals except that you could apply it to specific model numbers instead of everything.
Example command to do it for #1:
cartoon style #1 arrows false xsection round width 1 thick 1
Smoothing could be turned on/off with a separate command, e.g.:
cartoon #1 smooth 0 cartoon #1 smooth 1
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 5, 2022, at 9:09 AM, Mauricio Losilla via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hi all,
Thank you so much for your input. You are all correct, the issue was
with the beta-strand smoothening-- I don't think a new feature is required.
To clarify, ChimeraX thinks the purple ribbon is just a coil because...
I told it so, with setattr #1/t res ss_type 0
and the beta-smoothening of the gray chain explains the issue I was
having.
I apologize if this was confusing. I did this because, when the 2 chains
were displayed with helixes and strands, they looked blended with each other (see "chimerax_blended", attached). I don't like this look. By the way, I believe this cannot be changed by tweaking with cartoon smooth!
I am probably showcasing my naivete, but deleting this chain's secondary
structure was the only way I was able to show the protein only as a coil (without helixes and strands). Is there a better way to do this?
After your feedback, I used the transparency, cartoon, and cartoon style
commands to arrange a very satisfactory display ("new_result", attached).
Thank you all very much!
Regards, Mau
Mauricio Losilla, PhD Integrative Biology; and Ecology, Evolution, & Behavior Michigan State University he, him, his
On Tue, Apr 5, 2022 at 4:52 AM JAMES MICHAEL S1JJRUdFUiA= <
jmkrieger@cnb.csic.es> wrote:
Thanks Elaine. That's great. That's even better than pymol then where it's a global setting.
Elaine Meng meng@cgl.ucsf.edu escribió:
Hi James, Yes, ChimeraX has an option to turn off the beta-strand smoothing for specific residues/chains, or the whole structure. Example:
open 1www cartoon /Y smooth 0 cartoon smooth 0 cartoon smooth 1
...where the above shows doing it for chain Y only, then the whole structure, then changes back to the default smoothing of 1.0. You can also use intermediate values in the 0-1 range. Details in "cartoon" help: <
https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 4, 2022, at 4:19 AM, JAMES MICHAEL S1JJRUdFUiA= via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Perhaps, you could turn off the beta strand flattening like in pymol. That could be quite a nice feature in chimerax if it isn't already there.
I think it's perfectly understandable and expectable that if you show the purple protein as spaghetti rather than a proper cartoon with helices and strands then the Calpha atoms follow their direct path (with perhaps a little smoothing) and the view does not resemble a flattened beta strand representation.
Best wishes James
Tom Goddard via ChimeraX-users chimerax-users@cgl.ucsf.edu
escribió:
Hi Mauricio,
The weaving of the purple tubular ribbon back and forth across the gray beta-strands is because ChimeraX smooths the beta-strand path so it does not go exactly through the C-alpha atoms. Because when it goes exactly through the C-alpha atoms it looks like wavy bacon as you showed in your rainbow ribbon image, and most people like the smooth appearance better. Your purple ribbon is just a tube shape which suggests ChimeraX thinks it is all coil secondary structure with no beta strands, so it does not smooth the it, and it goes on the wavy path through the C-alpha atoms. I am not sure why ChimeraX thinks your purple model is all coil -- would need the data to know why.
If I-Tasser made the gray model from the purple and assuming it kept the backbone nearly in the same place, I am not sure what you are trying to show -- maybe just that the backbone did stay in the same place? At any rate, you could either figure out how to make ChimeraX recognized that the purple template has beta strands so those get smoothed. Or you could make ChimeraX not smooth the gray predicted structure strands by using the "smooth" option of the cartoon command.
https://urldefense.com/v3/__https://www.cgl.ucsf.edu/chimerax/docs/user/comm...
Tom
On Apr 1, 2022, at 5:43 PM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Oops, typed the wrong number, sorry -- the ticket is #6527
Elaine
> On Apr 1, 2022, at 5:40 PM, Elaine Meng via ChimeraX-users > chimerax-users@cgl.ucsf.edu wrote: > > For anybody who is interested, I made a feature request ticket
#6257.
> > However, now that I look carefully at your original image of the > desired visual outcome (ideal_display.png) I see that it also is > "threaded" in some places, e.g. where the rainbow ribbon is > cyan. However, it is a lot less noticeable than in the ChimeraX > image because the rainbow ribbon is paper thin, what we called > "flat" ribbon in Chimera. ChimeraX does not have this ribbon > style option, although you can approximate it by making the > thickness of the ribbon very small instead of the default 0.4 > Angstroms. > > I added this as a comment on the ticket. > Best, > Elaine > >> On Apr 1, 2022, at 2:20 PM, Mauricio Losilla via ChimeraX-users >> chimerax-users@cgl.ucsf.edu wrote: >> >> I understand. Thank you very much for your assistance! >> >> >> Mauricio Losilla, PhD >> Integrative Biology; and Ecology, Evolution, & Behavior >> Michigan State University >> he, him, his >> >> >> On Fri, Apr 1, 2022 at 10:06 AM Elaine Meng meng@cgl.ucsf.edu
wrote:
>> Hi Mauricio, >> Probably the "real" way to do it is to save two images, one of >> each chain with the other one hidden, and then use a separate >> image-editing app like Gimp or Photoshop to composite the two >> images together. I wonder if that is what the I-tasser folks >> did. >> >> The only other idea I had seemed like cheating, to actually >> Z-translate the purple model closer to the user. Also it might >> not look right, even if you change from perspective projection >> to orthoscopic (command "camera ortho") >> >> I am not a programmer so I would not be the one to figure out >> an algorithm or how feasible it would be to implement, i.e. >> I'll create a feature request ticket and put you on the >> notification list, but can't say anything about how it will be >> prioritized. >> Best, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >>> On Apr 1, 2022, at 8:17 AM, Mauricio Losilla via >>> ChimeraX-users chimerax-users@cgl.ucsf.edu wrote: >>> >>> Hi Elaine, >>> >>> I am sorry, I didn't explain myself well, I will try to do it >>> here. I was able to use all your tips successfully: I split >>> the chain in two models, and tweaked the thickness, width, and >>> transparency at will. It worked great! I am attaching the >>> result. I think it accomplishes my original goal fairly well: >>> to visually represent the fit of the gray protein to the >>> purple template. >>> >>> However, the purple chain still looks sewed into the gray >>> chain. In the image, this is better seen in the horizontal >>> beta sheets at the center. The ideal display I was after is >>> that of the image with the rainbow-colored chain and the >>> purple template I sent in my original email. There, the purple >>> chain always looks "on top" of the rainbow chain. That is what >>> I meant yesterday with "the ability to superimpose the view of >>> one chain". >>> >>> In case it is helpful, the reference image and the PDB file >>> came from I-TASSER. >>> >>> I am new to ChimeraX (and to 3D shapes of molecules in >>> general), so I apologize if I am not making much sense. >>> >>> Thank you! >>> >>> <result.png> >>> >>> >>> Mauricio Losilla, PhD >>> Integrative Biology; and Ecology, Evolution, & Behavior >>> Michigan State University >>> he, him, his >>> >>> >>> On Thu, Mar 31, 2022 at 5:11 PM Elaine Meng meng@cgl.ucsf.edu
wrote:
>>> Hi Mauricio, >>> I don't understand "the ability to superimpose the view of one >>> chain" -- can you explain it in more words? What is it that >>> you want, that cannot be done currently? Maybe it is already >>> possible but I didn't explain it because I didn't realize that >>> was what you wanted. >>> >>> If you mean to make "cartoon style" work on just a chain >>> instead of whole model, it may be unlikely since the settings >>> it controls are per-model (not per-chain or per-residue). >>> However, it is already easy to split chains into separate >>> models with "split." >>> >>> Sorry if I am misunderstanding what you meant, however. >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>>> On Mar 31, 2022, at 3:42 PM, Mauricio Losilla via >>>> ChimeraX-users chimerax-users@cgl.ucsf.edu wrote: >>>> >>>> Hi Elaine, >>>> >>>> Thank you very much for your prompt reply. Your workarounds >>>> were very helpful, I was able to tweak thickness and >>>> transparency, and arrived at a satisfactory display >>>> composition. Would you consider as a request feature the >>>> ability to superimpose the view of one chain? >>>> >>>> Thank you! >>>> Mau >>>> >>>> Mauricio Losilla, PhD >>>> Integrative Biology; and Ecology, Evolution, & Behavior >>>> Michigan State University >>>> he, him, his >>>> >>>> >>>> On Thu, Mar 31, 2022 at 11:43 AM Elaine Meng >>>> meng@cgl.ucsf.edu wrote: >>>> Hi Mauricio, >>>> Some ideas are to: >>>> >>>> - make the gray ribbon transparent >>>> and/or >>>> - make the purple one thicker >>>> >>>> I can't tell from your question whether they are in two >>>> separate models or not. Even if they're together in one PDB >>>> file they can be defined as separate models (as is done for >>>> NMR ensembles, e.g. PDB 1kfp). If the purple one is model #1 >>>> and the gray one is #2, could be something like: >>>> >>>> cartoon style #1 width 1 thick 1 xsect round >>>> transparency #2 50 targ r >>>> >>>> ...of course, you could use different width/thickness and >>>> transparency values. >>>> >>>> <
https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...
>>>> > >>>> <
https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...
>>>> >>>> The cartoon style command works on whole models, so you would >>>> need them to be in separate models for that approach. If >>>> your current PDB file does not have them in separate models, >>>> you could either text-edit it to add MODEL and ENDMDL >>>> records, or (probably easier) use the "split" command after >>>> opening it. >>>> <
https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...
>>>> > >>>> >>>> I hope this helps, >>>> Elaine >>>> ----- >>>> Elaine C. Meng, Ph.D. >>>> UCSF Chimera(X) team >>>> Department of Pharmaceutical Chemistry >>>> University of California, San Francisco >>>> >>>>> On Mar 31, 2022, at 10:02 AM, Mauricio Losilla via >>>>> ChimeraX-users chimerax-users@cgl.ucsf.edu wrote: >>>>> >>>>> Hi, >>>>> >>>>> I am new to ChimeraX, thank you for making this great >>>>> software available. >>>>> >>>>> I loaded a pdb file that has 2 amino acid chains aligned >>>>> (chimerax.png). These chains are a model (gray) and template >>>>> (purple). >>>>> >>>>> As you can see, the two chains look weaved or blended. I >>>>> would much prefer to display the uninterrupted template >>>>> around to model, to visually represent their fit. Is there a >>>>> way to do this? >>>>> >>>>> I am attaching a second image (ideal_display.png, generated >>>>> elsewhere) with the visual outcome I am after (the purple >>>>> chain is the template, the rainbow-colored chain is the >>>>> model). >>>>> >>>>> Thank you >>>>> Mauricio Losilla, PhD >>>>> Integrative Biology; and Ecology, Evolution, & Behavior >>>>> Michigan State University >>>>> he, him, his
<chimerax_blended.png><new_result.png>_______________________________________________
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