issues with ChimeraX

[shahid.mehmood@…]

Hello,
My name is Shahid and I am a senior scientist at Francis Crick Institute, London. I recently installed ChimeraX on my Windows 10 PC and it has been running fine without any issues. A week ago I installed a Xlink plugin to visualise Xlink data on the protein structure by using ChimeraX. Since the installation of the plugin I am unable to run ChimeraX, on running the program, first page with picture of developers group appears and then no response.  I even uninstalled the program and downloaded and installed but it did not help.

I was wondering if you could help me with this?

Many thanks


Shahid


The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT

[pett]

Hi Shahid,
I am unfamiliar with an "Xlink" plugin. I know there is an "Xlink Analyzer" plugin for _Chimera_ (not ChimeraX). Is that what you're referring to? Also, how did you install this plugin?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[shahid.mehmood@…]

Hi Eric
Thanks for quick reply. Sorry for the confusion, yes I am referring to xlink Analyser. I downloaded the plugin from following website and ran the exe. I didn’t realise that the plugin is for Chimera only.
What I should do now?

https://www.embl-hamburg.de/XlinkAnalyzer/XlinkAnalyzer.html

Shahid

Sent from my iPhone

On 2 Oct 2019, at 19:43, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:

#2464: issues with ChimeraX
---------------------------------------+----------------------------
         Reporter:  shahid.mehmood@…  |      Owner:  Eric Pettersen
             Type:  defect            |     Status:  accepted
         Priority:  normal            |  Milestone:
        Component:  Third Party       |    Version:
       Resolution:                    |   Keywords:
       Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
          Project:  ChimeraX          |
---------------------------------------+----------------------------
Changes (by Eric Pettersen):

* status:  new => accepted
* cc: Tom Goddard (added)
* component:  Unassigned => Third Party
* project:   => ChimeraX
* platform:   => all
* owner:  (none) => Eric Pettersen


Comment:

Hi Shahid,
       I am unfamiliar with an "Xlink" plugin.  I know there is an "Xlink
Analyzer" plugin for _Chimera_ (not ChimeraX).  Is that what you're
referring to?  Also, how did you install this plugin?

--Eric

        Eric Pettersen
        UCSF Computer Graphics Lab

--
Ticket URL: <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F2464%23comment%3A1&amp;data=02%7C01%7C%7Cf5bc3fe9c4354eb357a508d747687411%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637056386261660752&amp;sdata=u7jiSCgw4YcI1q48WmxFwT5PMnFHVLzwcEQ5A4CEjTs%3D&amp;reserved=0>
ChimeraX <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&amp;data=02%7C01%7C%7Cf5bc3fe9c4354eb357a508d747687411%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637056386261670747&amp;sdata=IXtvT%2FLgGafppaNk9QG%2FD7au%2B%2FPtxc1Wxac0T%2F63QC8%3D&amp;reserved=0>
ChimeraX Issue Tracker

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT

[pett]

I am at a loss as to what you did exactly. XlinkAnalyzer does not provide an exe as far as I can tell, and the installation instructions provide two methods, neither of which would work at all with ChimeraX (i.e. you would not be able to complete either one).

So, forget that. Try this: download ChimeraX again and install it into a _new_ location (i.e. do not overwrite an existing installation). Does that work, or does it fail in the same way?

[shahid.mehmood@…]

Hi Eric
Thank you for your help
I would like to use XlinkAnalyser plugin so should I install _Chimera_ instead of ChimeraX? And this installation would be in a new directory.
Best
Shahid

Sent from my iPhone

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT

[shahid.mehmood@…]

Hello
Thank you guys. I uninstalled ChimeraX and installed Chimera version 1.14 (build 42068) and it is working fine. I even managed to add Xlink Analyser plugin. It was added by adding utilities in tool menu.
So all sorted.
All the best
Shahid


-----Original Message-----
From: ChimeraX [mailto:ChimeraX-bugs-admin@cgl.ucsf.edu]
Sent: 03 October 2019 03:57
To: pett@cgl.ucsf.edu; Shahid Mehmood <shahid.mehmood@crick.ac.uk>
Cc: goddard@cgl.ucsf.edu
Subject: Re: [ChimeraX] #2464: issues with ChimeraX

#2464: issues with ChimeraX
---------------------------------------+----------------------------
          Reporter:  shahid.mehmood@…  |      Owner:  Eric Pettersen
              Type:  defect            |     Status:  feedback
          Priority:  normal            |  Milestone:
         Component:  Third Party       |    Version:
        Resolution:                    |   Keywords:
        Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
           Project:  ChimeraX          |
---------------------------------------+----------------------------

Comment (by shahid.mehmood@…):

 {{{
 Hi Eric
 Thank you for your help
 I would like to use XlinkAnalyser plugin so should I install _Chimera_  instead of ChimeraX? And this installation would be in a new directory.
 Best
 Shahid

 Sent from my iPhone

 The Francis Crick Institute Limited is a registered charity in England and  Wales no. 1140062 and a company registered in England and Wales no.
 06885462, with its registered office at 1 Midland Road London NW1 1AT  }}}

--
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ChimeraX <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&amp;data=02%7C01%7C%7Ccbce8909380a4f9686ab08d747ad54aa%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637056682109889299&amp;sdata=M2mZiE5vCzIZMBTjVqCBT3tr3vy1gMtIHkJ36E%2BUfZo%3D&amp;reserved=0>
ChimeraX Issue Tracker
The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT
}}}

[pett]

Yes, if what you want to do is use XLinkAnalyzer, then Chimera is the only way to go. Glad you got it all to work!

--Eric