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

[JAMES MICHAEL S1JJRUdFUiA=]

Hi Elaine,

It would be nice to have representation settings like "cartoon style"  
or "sticks" accessible on a per-chain or per-residue basis. This is a  
feature I use a lot in pymol and VMD.

Best wishes
James

Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> escribió:

> 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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