<meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr"><div>Hi Elaine,</div><div><br></div><div>thank you for the information, that is very helpful.</div><div><br></div>Mau<div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><b>Mauricio Losilla, PhD</b><br>Integrative Biology; and Ecology, Evolution, & Behavior<br>Michigan State University<br>he, him, his</div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Apr 5, 2022 at 10:28 AM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Mauricio,<br>
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.<br>
<br>
Example command to do it for #1:<br>
<br>
cartoon style #1 arrows false xsection round width 1 thick 1<br>
<br>
Smoothing could be turned on/off with a separate command, e.g.:<br>
<br>
cartoon #1 smooth 0<br>
cartoon #1 smooth 1<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Apr 5, 2022, at 9:09 AM, Mauricio Losilla via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
> <br>
> Hi all,<br>
> <br>
> 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. <br>
> <br>
> To clarify, ChimeraX thinks the purple ribbon is just a coil because... I told it so, with setattr #1/t res ss_type 0<br>
> and the beta-smoothening of the gray chain explains the issue I was having. <br>
> <br>
> 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! <br>
> <br>
> 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? <br>
> <br>
> After your feedback, I used the transparency, cartoon, and cartoon style commands to arrange a very satisfactory display ("new_result", attached).<br>
> <br>
> Thank you all very much!<br>
> <br>
> Regards,<br>
> Mau<br>
> <br>
> <br>
> Mauricio Losilla, PhD<br>
> Integrative Biology; and Ecology, Evolution, & Behavior<br>
> Michigan State University<br>
> he, him, his<br>
> <br>
> <br>
> On Tue, Apr 5, 2022 at 4:52 AM JAMES MICHAEL S1JJRUdFUiA= <<a href="mailto:jmkrieger@cnb.csic.es" target="_blank">jmkrieger@cnb.csic.es</a>> wrote:<br>
> Thanks Elaine. That's great. That's even better than pymol then where <br>
> it's a global setting.<br>
> <br>
> Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>> escribió:<br>
> <br>
> > Hi James,<br>
> > Yes, ChimeraX has an option to turn off the beta-strand smoothing <br>
> > for specific residues/chains, or the whole structure. Example:<br>
> ><br>
> > open 1www<br>
> > cartoon /Y smooth 0<br>
> > cartoon smooth 0<br>
> > cartoon smooth 1<br>
> ><br>
> > ...where the above shows doing it for chain Y only, then the whole <br>
> > structure, then changes back to the default smoothing of 1.0. You <br>
> > can also use intermediate values in the 0-1 range. Details in <br>
> > "cartoon" help:<br>
> > <<a href="https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html__;!!HXCxUKc!h1lhfqX3hUVl90-jAZnkZtp9opCBKFVH6f0VoDOYDEkLnLgRyJZ6PUl8I0xTisc$" rel="noreferrer" target="_blank">https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html__;!!HXCxUKc!h1lhfqX3hUVl90-jAZnkZtp9opCBKFVH6f0VoDOYDEkLnLgRyJZ6PUl8I0xTisc$</a> ><br>
> ><br>
> > Best,<br>
> > Elaine<br>
> > -----<br>
> > Elaine C. Meng, Ph.D.<br>
> > UCSF Chimera(X) team<br>
> > Department of Pharmaceutical Chemistry<br>
> > University of California, San Francisco<br>
> ><br>
> ><br>
> >> On Apr 4, 2022, at 4:19 AM, JAMES MICHAEL S1JJRUdFUiA= via <br>
> >> ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
> >><br>
> >> Perhaps, you could turn off the beta strand flattening like in <br>
> >> pymol. That could be quite a nice feature in chimerax if it isn't <br>
> >> already there.<br>
> >><br>
> >> I think it's perfectly understandable and expectable that if you <br>
> >> show the purple protein as spaghetti rather than a proper cartoon <br>
> >> with helices and strands then the Calpha atoms follow their direct <br>
> >> path (with perhaps a little smoothing) and the view does not <br>
> >> resemble a flattened beta strand representation.<br>
> >><br>
> >> Best wishes<br>
> >> James<br>
> >><br>
> >> Tom Goddard via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> escribió:<br>
> >><br>
> >>> Hi Mauricio,<br>
> >>><br>
> >>> The weaving of the purple tubular ribbon back and forth across <br>
> >>> the gray beta-strands is because ChimeraX smooths the beta-strand <br>
> >>> path so it does not go exactly through the C-alpha atoms. Because <br>
> >>> when it goes exactly through the C-alpha atoms it looks like wavy <br>
> >>> bacon as you showed in your rainbow ribbon image, and most people <br>
> >>> like the smooth appearance better. Your purple ribbon is just a <br>
> >>> tube shape which suggests ChimeraX thinks it is all coil secondary <br>
> >>> structure with no beta strands, so it does not smooth the it, and <br>
> >>> it goes on the wavy path through the C-alpha atoms. I am not sure <br>
> >>> why ChimeraX thinks your purple model is all coil -- would need <br>
> >>> the data to know why.<br>
> >>><br>
> >>> If I-Tasser made the gray model from the purple and assuming it <br>
> >>> kept the backbone nearly in the same place, I am not sure what you <br>
> >>> are trying to show -- maybe just that the backbone did stay in the <br>
> >>> same place? At any rate, you could either figure out how to make <br>
> >>> ChimeraX recognized that the purple template has beta strands so <br>
> >>> those get smoothed. Or you could make ChimeraX not smooth the <br>
> >>> gray predicted structure strands by using the "smooth" option of <br>
> >>> the cartoon command.<br>
> >>><br>
> >>> <a href="https://urldefense.com/v3/__https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cartoon.html__;!!HXCxUKc!h1lhfqX3hUVl90-jAZnkZtp9opCBKFVH6f0VoDOYDEkLnLgRyJZ6PUl8AeEsVj0$" rel="noreferrer" target="_blank">https://urldefense.com/v3/__https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cartoon.html__;!!HXCxUKc!h1lhfqX3hUVl90-jAZnkZtp9opCBKFVH6f0VoDOYDEkLnLgRyJZ6PUl8AeEsVj0$</a> <br>
> >>><br>
> >>> Tom<br>
> >>><br>
> >>><br>
> >>>> On Apr 1, 2022, at 5:43 PM, Elaine Meng via ChimeraX-users <br>
> >>>> <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
> >>>><br>
> >>>> Oops, typed the wrong number, sorry -- the ticket is #6527<br>
> >>>><br>
> >>>> Elaine<br>
> >>>><br>
> >>>>> On Apr 1, 2022, at 5:40 PM, Elaine Meng via ChimeraX-users <br>
> >>>>> <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
> >>>>><br>
> >>>>> For anybody who is interested, I made a feature request ticket #6257.<br>
> >>>>><br>
> >>>>> However, now that I look carefully at your original image of the <br>
> >>>>> desired visual outcome (ideal_display.png) I see that it also is <br>
> >>>>> "threaded" in some places, e.g. where the rainbow ribbon is <br>
> >>>>> cyan. However, it is a lot less noticeable than in the ChimeraX <br>
> >>>>> image because the rainbow ribbon is paper thin, what we called <br>
> >>>>> "flat" ribbon in Chimera. ChimeraX does not have this ribbon <br>
> >>>>> style option, although you can approximate it by making the <br>
> >>>>> thickness of the ribbon very small instead of the default 0.4 <br>
> >>>>> Angstroms.<br>
> >>>>><br>
> >>>>> I added this as a comment on the ticket.<br>
> >>>>> Best,<br>
> >>>>> Elaine<br>
> >>>>><br>
> >>>>>> On Apr 1, 2022, at 2:20 PM, Mauricio Losilla via ChimeraX-users <br>
> >>>>>> <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
> >>>>>><br>
> >>>>>> I understand. Thank you very much for your assistance!<br>
> >>>>>><br>
> >>>>>><br>
> >>>>>> Mauricio Losilla, PhD<br>
> >>>>>> Integrative Biology; and Ecology, Evolution, & Behavior<br>
> >>>>>> Michigan State University<br>
> >>>>>> he, him, his<br>
> >>>>>><br>
> >>>>>><br>
> >>>>>> On Fri, Apr 1, 2022 at 10:06 AM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>> wrote:<br>
> >>>>>> Hi Mauricio,<br>
> >>>>>> Probably the "real" way to do it is to save two images, one of <br>
> >>>>>> each chain with the other one hidden, and then use a separate <br>
> >>>>>> image-editing app like Gimp or Photoshop to composite the two <br>
> >>>>>> images together. I wonder if that is what the I-tasser folks <br>
> >>>>>> did.<br>
> >>>>>><br>
> >>>>>> The only other idea I had seemed like cheating, to actually <br>
> >>>>>> Z-translate the purple model closer to the user. Also it might <br>
> >>>>>> not look right, even if you change from perspective projection <br>
> >>>>>> to orthoscopic (command "camera ortho")<br>
> >>>>>><br>
> >>>>>> I am not a programmer so I would not be the one to figure out <br>
> >>>>>> an algorithm or how feasible it would be to implement, i.e. <br>
> >>>>>> I'll create a feature request ticket and put you on the <br>
> >>>>>> notification list, but can't say anything about how it will be <br>
> >>>>>> prioritized.<br>
> >>>>>> Best,<br>
> >>>>>> Elaine<br>
> >>>>>> -----<br>
> >>>>>> Elaine C. Meng, Ph.D.<br>
> >>>>>> UCSF Chimera(X) team<br>
> >>>>>> Department of Pharmaceutical Chemistry<br>
> >>>>>> University of California, San Francisco<br>
> >>>>>><br>
> >>>>>><br>
> >>>>>>> On Apr 1, 2022, at 8:17 AM, Mauricio Losilla via <br>
> >>>>>>> ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
> >>>>>>><br>
> >>>>>>> Hi Elaine,<br>
> >>>>>>><br>
> >>>>>>> I am sorry, I didn't explain myself well, I will try to do it <br>
> >>>>>>> here. I was able to use all your tips successfully: I split <br>
> >>>>>>> the chain in two models, and tweaked the thickness, width, and <br>
> >>>>>>> transparency at will. It worked great! I am attaching the <br>
> >>>>>>> result. I think it accomplishes my original goal fairly well: <br>
> >>>>>>> to visually represent the fit of the gray protein to the <br>
> >>>>>>> purple template.<br>
> >>>>>>><br>
> >>>>>>> However, the purple chain still looks sewed into the gray <br>
> >>>>>>> chain. In the image, this is better seen in the horizontal <br>
> >>>>>>> beta sheets at the center. The ideal display I was after is <br>
> >>>>>>> that of the image with the rainbow-colored chain and the <br>
> >>>>>>> purple template I sent in my original email. There, the purple <br>
> >>>>>>> chain always looks "on top" of the rainbow chain. That is what <br>
> >>>>>>> I meant yesterday with "the ability to superimpose the view of <br>
> >>>>>>> one chain".<br>
> >>>>>>><br>
> >>>>>>> In case it is helpful, the reference image and the PDB file <br>
> >>>>>>> came from I-TASSER.<br>
> >>>>>>><br>
> >>>>>>> I am new to ChimeraX (and to 3D shapes of molecules in <br>
> >>>>>>> general), so I apologize if I am not making much sense.<br>
> >>>>>>><br>
> >>>>>>> Thank you!<br>
> >>>>>>><br>
> >>>>>>> <result.png><br>
> >>>>>>><br>
> >>>>>>><br>
> >>>>>>> Mauricio Losilla, PhD<br>
> >>>>>>> Integrative Biology; and Ecology, Evolution, & Behavior<br>
> >>>>>>> Michigan State University<br>
> >>>>>>> he, him, his<br>
> >>>>>>><br>
> >>>>>>><br>
> >>>>>>> On Thu, Mar 31, 2022 at 5:11 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>> wrote:<br>
> >>>>>>> Hi Mauricio,<br>
> >>>>>>> I don't understand "the ability to superimpose the view of one <br>
> >>>>>>> chain" -- can you explain it in more words? What is it that <br>
> >>>>>>> you want, that cannot be done currently? Maybe it is already <br>
> >>>>>>> possible but I didn't explain it because I didn't realize that <br>
> >>>>>>> was what you wanted.<br>
> >>>>>>><br>
> >>>>>>> If you mean to make "cartoon style" work on just a chain <br>
> >>>>>>> instead of whole model, it may be unlikely since the settings <br>
> >>>>>>> it controls are per-model (not per-chain or per-residue). <br>
> >>>>>>> However, it is already easy to split chains into separate <br>
> >>>>>>> models with "split."<br>
> >>>>>>><br>
> >>>>>>> Sorry if I am misunderstanding what you meant, however.<br>
> >>>>>>> Elaine<br>
> >>>>>>> -----<br>
> >>>>>>> Elaine C. Meng, Ph.D.<br>
> >>>>>>> UCSF Chimera(X) team<br>
> >>>>>>> Department of Pharmaceutical Chemistry<br>
> >>>>>>> University of California, San Francisco<br>
> >>>>>>><br>
> >>>>>>>> On Mar 31, 2022, at 3:42 PM, Mauricio Losilla via <br>
> >>>>>>>> ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
> >>>>>>>><br>
> >>>>>>>> Hi Elaine,<br>
> >>>>>>>><br>
> >>>>>>>> Thank you very much for your prompt reply. Your workarounds <br>
> >>>>>>>> were very helpful, I was able to tweak thickness and <br>
> >>>>>>>> transparency, and arrived at a satisfactory display <br>
> >>>>>>>> composition. Would you consider as a request feature the <br>
> >>>>>>>> ability to superimpose the view of one chain?<br>
> >>>>>>>><br>
> >>>>>>>> Thank you!<br>
> >>>>>>>> Mau<br>
> >>>>>>>><br>
> >>>>>>>> Mauricio Losilla, PhD<br>
> >>>>>>>> Integrative Biology; and Ecology, Evolution, & Behavior<br>
> >>>>>>>> Michigan State University<br>
> >>>>>>>> he, him, his<br>
> >>>>>>>><br>
> >>>>>>>><br>
> >>>>>>>> On Thu, Mar 31, 2022 at 11:43 AM Elaine Meng <br>
> >>>>>>>> <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>> wrote:<br>
> >>>>>>>> Hi Mauricio,<br>
> >>>>>>>> Some ideas are to:<br>
> >>>>>>>><br>
> >>>>>>>> - make the gray ribbon transparent<br>
> >>>>>>>> and/or<br>
> >>>>>>>> - make the purple one thicker<br>
> >>>>>>>><br>
> >>>>>>>> I can't tell from your question whether they are in two <br>
> >>>>>>>> separate models or not. Even if they're together in one PDB <br>
> >>>>>>>> file they can be defined as separate models (as is done for <br>
> >>>>>>>> NMR ensembles, e.g. PDB 1kfp). If the purple one is model #1 <br>
> >>>>>>>> and the gray one is #2, could be something like:<br>
> >>>>>>>><br>
> >>>>>>>> cartoon style #1 width 1 thick 1 xsect round<br>
> >>>>>>>> transparency #2 50 targ r<br>
> >>>>>>>><br>
> >>>>>>>> ...of course, you could use different width/thickness and <br>
> >>>>>>>> transparency values.<br>
> >>>>>>>><br>
> >>>>>>>> <<a href="https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html*style__;Iw!!HXCxUKc!hKsk6lXSWeI6B9WmfXcRKCWrq70659PcqAPq2FBwdZzjDjOH6myV44XapFhvyuc$" rel="noreferrer" target="_blank">https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html*style__;Iw!!HXCxUKc!hKsk6lXSWeI6B9WmfXcRKCWrq70659PcqAPq2FBwdZzjDjOH6myV44XapFhvyuc$</a> <br>
> >>>>>>>> ><br>
> >>>>>>>> <<a href="https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html__;!!HXCxUKc!hKsk6lXSWeI6B9WmfXcRKCWrq70659PcqAPq2FBwdZzjDjOH6myV44Xa-fKcbds$" rel="noreferrer" target="_blank">https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html__;!!HXCxUKc!hKsk6lXSWeI6B9WmfXcRKCWrq70659PcqAPq2FBwdZzjDjOH6myV44Xa-fKcbds$</a>><br>
> >>>>>>>><br>
> >>>>>>>> The cartoon style command works on whole models, so you would <br>
> >>>>>>>> need them to be in separate models for that approach. If <br>
> >>>>>>>> your current PDB file does not have them in separate models, <br>
> >>>>>>>> you could either text-edit it to add MODEL and ENDMDL <br>
> >>>>>>>> records, or (probably easier) use the "split" command after <br>
> >>>>>>>> opening it.<br>
> >>>>>>>> <<a href="https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html__;!!HXCxUKc!hKsk6lXSWeI6B9WmfXcRKCWrq70659PcqAPq2FBwdZzjDjOH6myV44XaI58NOwM$" rel="noreferrer" target="_blank">https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html__;!!HXCxUKc!hKsk6lXSWeI6B9WmfXcRKCWrq70659PcqAPq2FBwdZzjDjOH6myV44XaI58NOwM$</a> <br>
> >>>>>>>> ><br>
> >>>>>>>><br>
> >>>>>>>> I hope this helps,<br>
> >>>>>>>> Elaine<br>
> >>>>>>>> -----<br>
> >>>>>>>> Elaine C. Meng, Ph.D.<br>
> >>>>>>>> UCSF Chimera(X) team<br>
> >>>>>>>> Department of Pharmaceutical Chemistry<br>
> >>>>>>>> University of California, San Francisco<br>
> >>>>>>>><br>
> >>>>>>>>> On Mar 31, 2022, at 10:02 AM, Mauricio Losilla via <br>
> >>>>>>>>> ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
> >>>>>>>>><br>
> >>>>>>>>> Hi,<br>
> >>>>>>>>><br>
> >>>>>>>>> I am new to ChimeraX, thank you for making this great <br>
> >>>>>>>>> software available.<br>
> >>>>>>>>><br>
> >>>>>>>>> I loaded a pdb file that has 2 amino acid chains aligned <br>
> >>>>>>>>> (chimerax.png). These chains are a model (gray) and template <br>
> >>>>>>>>> (purple).<br>
> >>>>>>>>><br>
> >>>>>>>>> As you can see, the two chains look weaved or blended. I <br>
> >>>>>>>>> would much prefer to display the uninterrupted template <br>
> >>>>>>>>> around to model, to visually represent their fit. Is there a <br>
> >>>>>>>>> way to do this?<br>
> >>>>>>>>><br>
> >>>>>>>>> I am attaching a second image (ideal_display.png, generated <br>
> >>>>>>>>> elsewhere) with the visual outcome I am after (the purple <br>
> >>>>>>>>> chain is the template, the rainbow-colored chain is the <br>
> >>>>>>>>> model).<br>
> >>>>>>>>><br>
> >>>>>>>>> Thank you<br>
> >>>>>>>>> Mauricio Losilla, PhD<br>
> >>>>>>>>> Integrative Biology; and Ecology, Evolution, & Behavior<br>
> >>>>>>>>> Michigan State University<br>
> >>>>>>>>> he, him, his<br>
> <br>
> <br>
> <br>
> <chimerax_blended.png><new_result.png>_______________________________________________<br>
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</blockquote></div>