<meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr">Hi all,<div><br></div><div>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. </div><div><br></div><div>To clarify, ChimeraX thinks the purple ribbon is just a coil because... I told it so, with setattr #1/t res ss_type 0</div><div>and the beta-smoothening of the gray chain explains the issue I was having. </div><div><br></div><div>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! </div><div><br></div><div>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? </div><div><br></div><div>After your feedback, I used the transparency, cartoon, and cartoon style commands to arrange a very satisfactory display ("new_result", attached).</div><div><br></div><div>Thank you all very much!</div><div><br></div><div>Regards,<br>Mau</div><div><br></div><div></div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><b><br></b></div><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><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Apr 5, 2022 at 4:52 AM JAMES MICHAEL S1JJRUdFUiA= <<a href="mailto:jmkrieger@cnb.csic.es">jmkrieger@cnb.csic.es</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">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>
</blockquote></div>