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

Tue Apr 5 10:37:26 PDT 2022

Hi Elaine,

thank you for the information, that is very helpful.

Mau

*Mauricio Losilla, PhD*
Integrative Biology; and Ecology, Evolution, & Behavior
Michigan State University
he, him, his

On Tue, Apr 5, 2022 at 10:28 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Mauricio,
> You definitely can show specific model(s) like spaghetti or licorice
> without changing their secondary structure assignments -- just make the
> width and cross-section of all protein cartoon the same with "cartoon
> style".  E.g. like menu: Presets... Licorice/Ovals except that you could
> apply it to specific model numbers instead of everything.
>
> Example command to do it for #1:
>
> cartoon style #1 arrows false xsection round width 1 thick 1
>
> Smoothing could be turned on/off with a separate command, e.g.:
>
> cartoon #1 smooth 0
> cartoon #1 smooth 1
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Apr 5, 2022, at 9:09 AM, Mauricio Losilla via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Hi all,
> >
> > Thank you so much for your input. You are all correct, the issue was
> with the beta-strand smoothening-- I don't think a new feature is required.
> >
> > To clarify, ChimeraX thinks the purple ribbon is just a coil because...
> I told it so, with setattr #1/t res ss_type 0
> > and the beta-smoothening of the gray chain explains the issue I was
> having.
> >
> > I apologize if this was confusing. I did this because, when the 2 chains
> were displayed with helixes and strands, they looked blended with each
> other (see "chimerax_blended", attached). I don't like this look. By the
> way, I believe this cannot be changed by tweaking with cartoon smooth!
> >
> > I am probably showcasing my naivete, but deleting this chain's secondary
> structure was the only way I was able to show the protein only as a coil
> (without helixes and strands). Is there a better way to do this?
> >
> > After your feedback, I used the transparency, cartoon, and cartoon style
> commands to arrange a very satisfactory display ("new_result", attached).
> >
> > Thank you all very much!
> >
> > Regards,
> > Mau
> >
> >
> > Mauricio Losilla, PhD
> > Integrative Biology; and Ecology, Evolution, & Behavior
> > Michigan State University
> > he, him, his
> >
> >
> > On Tue, Apr 5, 2022 at 4:52 AM JAMES MICHAEL S1JJRUdFUiA= <
> jmkrieger at cnb.csic.es> wrote:
> > 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://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html__;!!HXCxUKc!h1lhfqX3hUVl90-jAZnkZtp9opCBKFVH6f0VoDOYDEkLnLgRyJZ6PUl8I0xTisc$
> >
> > >
> > > 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://urldefense.com/v3/__https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cartoon.html__;!!HXCxUKc!h1lhfqX3hUVl90-jAZnkZtp9opCBKFVH6f0VoDOYDEkLnLgRyJZ6PUl8AeEsVj0$
> > >>>
> > >>>  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
> >
> >
> >
> >
> <chimerax_blended.png><new_result.png>_______________________________________________
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