[Chimera-users] A specific request for visualizing a model in Chimera

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 24 11:11:39 PST 2022

See for example the "thickened ribbon" examples in this nice publication:

Da Veiga Beltrame, E., Tyrwhitt-Drake, J., Roy, I., Shalaby, R., Suckale, J., Pomeranz Krummel, D. 3D Printing of Biomolecular Models for Research and Pedagogy. <em>J. Vis. Exp.</em> (121), e55427, doi:10.3791/55427 (2017).

They used the Chimera tool "Ribbon Style Editor."


> On Jan 24, 2022, at 11:03 AM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hi Qian,
> I don't know of any way to "smooth" those junctions between coil and helix/strand, but I believe that many people 3D print the ribbons and they have not been a problem as long as you make the overall ribbon thick enough, e.g. with the "struts" command or Ribbon Style Editor.
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/struts.html>
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html>
> Although I've seen it in other programs, Chimera does not have an option to smoothly taper the ribbon between coil and helix/strand.
> In general we recommend sending questions to the mailing list CC'd here, but only if you are not including private data.  In this case I don't think it matters what protein structure is involved, so it is a general question ... to which I don't have an answer but maybe others on the list will.  I did not include your session in this public message.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Jan 24, 2022, at 9:37 AM, Qian Zhang <qzhang30 at gmail.com> wrote:
>> Dear Dr. Meng,
>> I hope you are doing well. I emailed you guys about 4 years ago and got someone to help me write a script to do this but I can't find that script anymore.
>> What I wanted to achieve is to 'smooth' out the connections between random coil vs. helixes or vs. sheets.  Not like the one shown in this picture that the coil just inserts into the start of the sheet. 
>> <image.png>
>> I've attached a session file (v.1.15) that can be used as a starting point. 
>> The purpose of this is to 3D-print this into a structure and I am afraid all those non-smooth connections are going to break off. 
>> Please let me know.
>> Qian
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