[chimerax-users] display options for model with 2 chains
Tom Goddard
goddard at sonic.net
Fri Apr 1 20:13:25 PDT 2022
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://www.cgl.ucsf.edu/chimerax/docs/user/commands/cartoon.html
Tom
> On Apr 1, 2022, at 5:43 PM, Elaine Meng via ChimeraX-users <chimerax-users at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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/commands/cartoon.html*style__;Iw!!HXCxUKc!hKsk6lXSWeI6B9WmfXcRKCWrq70659PcqAPq2FBwdZzjDjOH6myV44XapFhvyuc$ >
>>>>> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html__;!!HXCxUKc!hKsk6lXSWeI6B9WmfXcRKCWrq70659PcqAPq2FBwdZzjDjOH6myV44Xa-fKcbds$>
>>>>>
>>>>> The cartoon style command works on whole models, so you would need them to be in separate models for that approach. If your current PDB file does not have them in separate models, you could either text-edit it to add MODEL and ENDMDL records, or (probably easier) use the "split" command after opening it.
>>>>> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html__;!!HXCxUKc!hKsk6lXSWeI6B9WmfXcRKCWrq70659PcqAPq2FBwdZzjDjOH6myV44XaI58NOwM$ >
>>>>>
>>>>> 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 at 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
>>>>>> <ideal_display.png><chimerax.png>
>>>>
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