[chimerax-users] display options for model with 2 chains

JAMES MICHAEL S1JJRUdFUiA= jmkrieger at cnb.csic.es
Tue Apr 5 03:52:40 PDT 2022 

Thanks Elaine. That's great. That's even better than pymol then where  
it's a global setting.

Elaine Meng <meng at 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://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html>
>
> 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 at 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 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

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