VMD-L Mailing List

From: Maud Jusot (maud.jusot_at_iktos.com)
Date: Thu Feb 22 2024 - 04:50:26 CST

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
>>
>>
>>
>>
>>
>>
>>
>>
>>