VMD-L Mailing List

From: Maud Jusot (maud.jusot_at_iktos.com)
Date: Thu Feb 22 2024 - 11:12:16 CST

Hi Barry,

I simply double-click on the VMD app icon in the Finder. I didn't try any
other way.

Cheers,
Maud

On Thu, 22 Feb 2024 at 16:45, Isralewitz, Barry <isralewi_at_illinois.edu>
wrote:

> Hi Maud.
>
> Thanks much for the details and file.
>
> An additional question: how are you launching VMD on your Mac? Do you
> double-click the VMD app icon in the Finder, are you typing a command into
> Terminal, or do you do something else? "Something else"examples:
> double-clicking on an alias you've made in the Finder, using Spotlight
> search, using some non-Spotlight launcher like Alfred or Quicksilver.
>
> Cheers,
> Barry
>
> On Feb 22, 2024, at 5:50 AM, Maud Jusot <maud.jusot_at_iktos.com> wrote:
>
> Hi again,
>
> I just wanted to add: my colleague didn't make the bug correction but she
> turned off her computer yesterday and this morning she installed VMD again
> and it was working without the fix. I suppose when she turned off the
> computer, an automated update solved the issue.
>
> Cheers,
> Maud
>
> On Thu, 22 Feb 2024 at 11:32, Maud Jusot <maud.jusot_at_iktos.com> wrote:
>
>> Hi Barry,
>>
>> 1) I'm on MacOS Ventura (v13.6.3) but my colleague was on a different
>> laptop on MacOS Sonoma (v14.2.1).
>> 2) I don't remember making any update on my computer between the
>> successful version and the one with the bug. Same for my colleague. But
>> maybe we didn't pay attention to it. And I'm definitely sure I didn't
>> change anything regarding VMD. And both of us tried to reinstall VMD when
>> we realized it was not working anymore and it didn't solve the problem.
>>
>> I attached the corrected startup.command file. Basically I just added a
>> "/" before the path to make it work.
>>
>> Let me know if you need any other details.
>>
>> Cheers,
>> Maud
>>
>> On Wed, 21 Feb 2024 at 19:07, Isralewitz, Barry <isralewi_at_illinois.edu>
>> wrote:
>>
>>> Hello Maud,
>>>
>>> Thanks for the bug report. I have two questions:
>>> 1) Which version of macOS are you running?
>>> 2) Did you make any changes / upgrades to this machine -- including to
>>> the VMD bundle directory -- between the most recent successful (unaltered)
>>> VMD launch and when you encountered this bug?
>>>
>>> Also, a bonus question: were your colleagues who also encountered
>>> this problem using the same machine as you? If not, I'd be interested in
>>> the answers to questions 1) and 2) for one or two of them.
>>>
>>> And, this request: could you send, as an email attachment , the version
>>> of startup.command that fixed the problem for you? I'm not following
>>> the differences and line breaks, versus the shipped version, in the edited
>>> version that you pasted in your email text.
>>>
>>> Cheers,
>>> Barry
>>>
>>>
>>> On Feb 21, 2024, at 9:24 AM, Maud Jusot <maud.jusot_at_iktos.com> wrote:
>>>
>>> Hello,
>>>
>>> It seems there is a bug when starting VMD (version 1.9.4 on MACOS ARM).
>>> It was working fine a few days ago but not anymore and was the same for a
>>> few colleagues. When running the application I got the following error:
>>>
>>> '''
>>> Applications/VMD\
>>> 1.9.4a57-arm64-Rev12.app/Contents/MacOS/startup.command
>>> <https://urldefense.com/v3/__http://1.9.4a57-arm64-Rev12.app/Contents/MacOS/startup.command__;!!DZ3fjg!7eKV6NDHVKgBpFKmy1-rNBYefCsakbmti334M2iYaKfy_0ukhZcooTCnmpUVZsZti52RAuUssQ-VuTjDl8sG$>
>>> ; exit;
>>> zsh: no such file or directory: Applications/VMD
>>> 1.9.4a57-arm64-Rev12.app/Contents/MacOS/startup.command
>>> <https://urldefense.com/v3/__http://1.9.4a57-arm64-Rev12.app/Contents/MacOS/startup.command__;!!DZ3fjg!7eKV6NDHVKgBpFKmy1-rNBYefCsakbmti334M2iYaKfy_0ukhZcooTCnmpUVZsZti52RAuUssQ-VuTjDl8sG$>
>>>
>>> '''
>>>
>>> It seems the path is not recognized correctly anymore. To solve it, I
>>> simply edit the `startup.command` as follow:
>>> '''
>>> #!/bin/sh # startup.command # This is the script executed by VMDLauncher
>>> to actually start VMD. p=`dirname "$0"`
>>> /"$p/../Resources/VMD.app/Contents/MacOS/VMD" $* '''
>>>
>>> Hope this can help,
>>>
>>> Best,
>>> Maud
>>>
>>>
>>>
>>> --
>>> Barry Isralewitz
>>> Theoretical and Computational Biophysics Group
>>> 3143 Beckman, University of Illinois at Urbana-Champaign
>>> Work Phone: (217) 300-1988
>>> Email: isralewi_at_illinois.edu
>>> https://www.ks.uiuc.edu/~barryi
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
> --
> Barry Isralewitz
> Theoretical and Computational Biophysics Group
> 3143 Beckman, University of Illinois at Urbana-Champaign
> Work Phone: (217) 300-1988
> Email: isralewi_at_illinois.edu
> https://www.ks.uiuc.edu/~barryi
>
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