[Chimera-users] [chimerax-users] Ramachandran Map in ChimeraX?

[Ralph Loring]

Thanks Tristan!  Unfortunately, the students tell me that the 1 GB size of
ChimeraX is about what their laptops can handle, so I'm reluctant to
require them to install another program to do a small part of a larger
exercise.  Hopefully ChimeraX will have a Ramachandran plot at some point
in the future, but I'll have other things for the students to do this year.
Ralph

On Wed, Jan 12, 2022 at 11:55 AM Tristan Croll <tic20 at cam.ac.uk> wrote:

> Hi all,
>
> Yep - ISOLDE certainly does have a Ramachandran plot (a rather pretty one,
> I like to think!). See
> https://isolde.cimr.cam.ac.uk/static/isolde/doc/tools/gui/validate.html#the-ramachandran-plot
> .
>
> Best regards,
> Tristan
> ------------------------------
> *From:* ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of
> Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
> *Sent:* 12 January 2022 16:50
> *To:* Ralph Loring <rhloring at gmail.com>
> *Cc:* ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>;
> chimera-users at cgl.ucsf.edu List <chimera-users at cgl.ucsf.edu>
> *Subject:* [chimerax-users] Ramachandran Map in ChimeraX?
>
> Hi Ralph,
> A missing tool (something in Chimera but not ChimeraX) should not be
> interpreted as intentionally chosen to be dropped... instead we may not
> have had time yet to add it.  It's certainly fine to ask on this mailing
> list, and good for us to hear which features users are most eager to have
> in ChimeraX.
>
> Since ChimeraX is built using entirely different frameworks than Chimera,
> tools need to be reimplemented mostly from scratch rather than simply
> copied and slotted in.  We have somewhat limited manpower. Consider that
> Chimera tools were added over 15-20 years!
>
> As for Ramachandran maps specifically, there may be something like that in
> the ISOLDE plugin.  ISOLDE is generally for rather advanced users building
> atomic structures into cryoEM density, but I can investigate whether it
> could simply be used to show a Ramachandran map for protein structures and
> how difficult that might be for somebody at the student level.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Jan 12, 2022, at 5:41 AM, Ralph Loring <rhloring at gmail.com> wrote:
> >
> > Hi, I'm updating protein problems for the upcoming semester and
> translating the instructions from Chimera to ChimeraX.  I can't find the
> Ramachandran plot in ChimeraX.  Is there an add-in that I'm missing?  I
> don't see it mentioned in the guide and can't find it in the help section.
> If it's not there, is there a reason it was dropped?  The students find it
> instructive.
> > Thanks,
> > Ralph
> >
> >
> > Ralph H. Loring
> > Associate Professor of Pharmacology
> > Department of Pharmaceutical Sciences
> > 166 TF
> > Northeastern University
> > 360 Huntington Avenue
> > Boston, MA 02115 USA
> > 617-373-3216 office
> > 617-373-8886 fax
> > r.loring at northeastern.edu
> >
>
>
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