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

Fri Apr 1 14:20:29 PDT 2022

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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