[phenixbb] unable to run coot

Werther, Rachel A rwerther at fredhutch.org
Thu Feb 11 15:42:43 PST 2021

Hello Maulik,

Sometimes uninstalling Xquartz and reinstalling it will correct the link between Phenix and Coot, particularly after computer updates.

Best of luck,

Rachel Werther / she & her pronouns / Research Technician III / Campbell Lab / Lab A3-201 / 206-667-4189 / Basic Sciences Division / Fred Hutchinson Cancer Research Center / rwerther at fredhutch.org<mailto:rwerther at fredhutch.org>

From: <phenixbb-bounces at phenix-online.org> on behalf of "Badmalia, Maulik" <maulik.badmalia at uleth.ca>
Date: Thursday, February 11, 2021 at 3:37 PM
To: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
Subject: [phenixbb] unable to run coot

hello team phenix,

I hope this email finds you well.

I recently downloaded phenix for analysing our cryoEM data, before moving to the data analysis I decided to try the tutorial. I decided to use the autosharpen option first, I was able to access the tutorial but when I clicked on coot I repeatedly got a message saying that "Sorry: the 'coot' command could not be located.

We have installed Coot to run on a CentOS platform and has the latest version of Coot on the system. I am a novice with linux and phenix. So any help in this regard would be highly appreciated. Do let me know if you have any questions.


Maulik D. Badmalia

Postdoctoral Researcher

Laboratory of Medicinal Biophysics

Alberta RNA Research and Training Institute

Dept. of Chemistry & Biochemistry

University of Lethbridge, Lethbridge, AB, Canada

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