[chimerax-users] display options for model with 2 chains
JAMES MICHAEL S1JJRUdFUiA=
jmkrieger at cnb.csic.es
Mon Apr 4 04:19:14 PDT 2022
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 at 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://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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