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

Qian Zhang qzhang30 at gmail.com
Mon Jan 24 11:26:08 PST 2022

Hi Dr. Meng,
I know Chimera doesn't have this function but a few years ago you
referred me to another person (maybe Dr. Huang? I can't remember) who
actually wrote a few lines of python code that did exactly what I needed.
He emailed me the script and I ran it by Chimera. I left that company so I
can't find the email anymore.

I already used Ribbon Style Editor to get to this step, if I can't figure
it out then we will live with this version. Any chance Dr. Huang can look
at this problem?


On Mon, Jan 24, 2022 at 2:03 PM Elaine Meng <meng 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.
> 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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