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

[Qian Zhang]

I will try out! Thanks.

On Mon, Jan 24, 2022 at 3:22 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> By the way, I just noticed that there is a bug in the "struts" command of
> Chimera that makes the ribbon arrowheads backwards.  However, we are no
> longer developing Chimera, so it is unlikely to be fixed.
>
> So if using Chimera, you should use Ribbon Style Editor to thicken the
> ribbons as described in that JoVE protocol link I sent earlier today.
>
> If you want to use the "struts" command, use ChimeraX instead of Chimera.
> The ChimeraX struts command does not have this bug.
>
> Elaine
>
> > On Jan 24, 2022, at 11:56 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > Sorry, he retired a couple of years ago!
> >
> > I looked in the archive for chimera-users at cgl.ucsf.edu and didn't find
> anything, but maybe you did  not communicate over this forum.  (Another
> advantage of using this address is the archive!)
> > <https://www.rbvi.ucsf.edu/chimera/docs/feedback.html>
> >
> > Elaine
> >
> >> On Jan 24, 2022, at 11:26 AM, Qian Zhang via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >>
> >> 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?
> >>
> >> Qian
> >>
> >> 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.
> >>>
> >>> <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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> >
>
>
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