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

Tristan Croll tic20 at cam.ac.uk
Wed Jan 12 09:20:53 PST 2022

No problem! For the record, ISOLDE adds another ~200 MB - but the installation is fairly trivial via the ChimeraX ToolShed (Tools/More Tools in the menu).

-- Tristan
From: Ralph Loring <rhloring at gmail.com>
Sent: 12 January 2022 17:17
To: Tristan Croll <tic20 at cam.ac.uk>
Cc: Tom Goddard via ChimeraX-users <chimerax-users at cgl.ucsf.edu>; Elaine Meng <meng at cgl.ucsf.edu>; chimera-users at cgl.ucsf.edu List <chimera-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Ramachandran Map in ChimeraX?

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.

On Wed, Jan 12, 2022 at 11:55 AM Tristan Croll <tic20 at cam.ac.uk<mailto: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,
From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu<mailto:chimerax-users-bounces at cgl.ucsf.edu>> on behalf of Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>>
Sent: 12 January 2022 16:50
To: Ralph Loring <rhloring at gmail.com<mailto:rhloring at gmail.com>>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>>; chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> List <chimera-users at cgl.ucsf.edu<mailto: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 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<mailto: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<mailto:r.loring at northeastern.edu>

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