VMD-L Mailing List

From: Phillip Compeau (pcompeau_at_andrew.cmu.edu)
Date: Mon Dec 20 2021 - 17:22:00 CST

Awesome, thank so much John! Please let me know when you get it resolved
and I can double-check and update on my end.

Phillip

On 12/20/21 12:51 AM, John Stone wrote:
> Phillip,
> We have made changes to Multiseq that have addressed the issues
> with STAMP on MacOS, however there is a problem that occurs on
> 64-bit Windows that I'm still working on tracking down.
> I plan to make new test builds of VMD in early January, possibly
> even before then, and I'll let you know what the status of STAMP is
> at that point.
>
> Best,
> John
>
> On Fri, Dec 17, 2021 at 11:58:45AM -0600, Phillip Compeau wrote:
>> Hi John,
>>
>> Just letting you know that my course is now published at
>> [1]https://urldefense.com/v3/__https://biologicalmodeling.org__;!!DZ3fjg!rct3fet-_-p2VA4eEuS5F8gCIMT2uyOCnqCmFUlaacktwbBhyaMyva-9WTwuvhLL$ . Please let me know when you think
>> there's a fix to multiseq. As of the moment, I'm indicating that stamp
>> alignment isn't working on the appropriate page.
>>
>> Thanks!
>>
>> Phillip
>>
>> On 12/3/21 9:22 AM, Phillip Compeau wrote:
>>
>> OK, thanks John!
>>
>> On 12/3/21 12:55 AM, John Stone wrote:
>>
>> Hi,
>> Actually, in general it is best to post to the mailing list,
>> because it often causes other users to comment about their
>> experiences. In this case, your email caused someone else
>> to report a different problem that also affected multiseq.
>> If you hadn't posted to the mailing list, they may not have
>> reported it. I'm thankful that they did, because we'll likely
>> be able to fix both issues at the same time...
>>
>> Best,
>> John Stone
>>
>>
>> On Thu, Dec 02, 2021 at 05:16:11PM -0500, Phillip Compeau wrote:
>>
>> Hi John,
>>
>> Thanks so much for following up! In the meantime I will let students know
>> that this is in the process of being fixed.
>>
>> Should I report any subsequent issues to you directly? I'm no longer
>> CC-ing the mailing list to avoid clogging folks' inboxes.
>>
>> Phillip
>>
>> On 12/2/21 3:32 PM, John Stone wrote:
>>
>> Hi Phillip,
>> We dug into the multiseq code today and indeed, there are some
>> issues with it's conficting use of both "grid" and "pack" GUI layout
>> managers that is almost certainly the cause of the hang you've seen.
>>
>> One of my colleagues here has volunteered to make an attempt at
>> addressing these bugs since the original authors no longer
>> support the code. I'm hoping we can have relatively rapid turnaround
>> on a fix for this now that we've discovered some obvious underlying issues
>> that need to be corrected.
>>
>> Best,
>> John Stone
>> [[2]1]vmd_at_ks.uiuc.edu
>>
>> On Wed, Dec 01, 2021 at 12:42:12AM -0600, John Stone wrote:
>>
>> Hi,
>> I'm guessing that this hang is caused by some bug in the multiseq
>> plugin related to its use of Tk, but that is only a guess.
>> Do you see any error messages in the main VMD console associated
>> with the hanging behavior, or is the hang the only observable behavior?
>>
>> Best,
>> John Stone
>> [[3]2]vmd_at_ks.uiuc.edu
>>
>> On Fri, Nov 26, 2021 at 11:05:02PM -0500, Phillip Compeau wrote:
>>
>> Hi,
>>
>> I am integrating VMD into a publicly available assignment that I
>> provide to my course as well ([3][4]https://urldefense.com/v3/__https://compeau.cbd.cmu.edu/online-education/sars-cov-2-protein-analysis-assignment/__;!!DZ3fjg!pDclAv9hZA92L09-ahO0FM6uDcyFOGbfeoCQpKkV1Rz8lrsqL5MxWaVg_EjA4Hs4cg$
>> ).
>>
>> As part of this, students are asked to, in the MultiSeq window,
>> select Tools -> STAMP alignment options -> ok to perform a STAMP
>> alignment with the default settings. However, this freezes for my
>> students. At first I thought this was Windows only but it seems to
>> affect both Windows and Mac.
>>
>> Thanks for your help! I'm not sure where else would make sense to
>> report this issue.
>>
>> Regards,
>>
>> Phillip Compeau
>>
>> --
>> NIH Center for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> [4][5]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> [5][6]http://www.ks.uiuc.edu/Research/vmd/
>>
>> References
>>
>> Visible links
>> 1. [7]mailto:vmd_at_ks.uiuc.edu
>> 2. [8]mailto:vmd_at_ks.uiuc.edu
>> 3. [9]https://urldefense.com/v3/__https://compeau.cbd.cmu.edu/online-education/sars-cov-2-protein-analysis-assignment/__;!!DZ3fjg!pDclAv9hZA92L09-ahO0FM6uDcyFOGbfeoCQpKkV1Rz8lrsqL5MxWaVg_EjA4Hs4cg$
>> 4. [10]http://www.ks.uiuc.edu/~johns/
>> 5. [11]http://www.ks.uiuc.edu/Research/vmd/
>>
>> References
>>
>> Visible links
>> 1.https://urldefense.com/v3/__https://biologicalmodeling.org__;!!DZ3fjg!us8dKpenTEr3SJAk2wpC9VONEjKxLHoltzlMXkkccxHGhoz20WVC-pXQqdIrZgBn$
>> 2.mailto:1]vmd_at_ks.uiuc.edu
>> 3.mailto:2]vmd_at_ks.uiuc.edu
>> 4.https://urldefense.com/v3/__https://compeau.cbd.cmu.edu/online-education/sars-cov-2-protein-analysis-assignment/__;!!DZ3fjg!pDclAv9hZA92L09-ahO0FM6uDcyFOGbfeoCQpKkV1Rz8lrsqL5MxWaVg_EjA4Hs4cg$
>> 5.http://www.ks.uiuc.edu/~johns/
>> 6.http://www.ks.uiuc.edu/Research/vmd/
>> 7.mailto:vmd_at_ks.uiuc.edu
>> 8.mailto:vmd_at_ks.uiuc.edu
>> 9.https://urldefense.com/v3/__https://compeau.cbd.cmu.edu/online-education/sars-cov-2-protein-analysis-assignment/__;!!DZ3fjg!pDclAv9hZA92L09-ahO0FM6uDcyFOGbfeoCQpKkV1Rz8lrsqL5MxWaVg_EjA4Hs4cg$
>> 10.http://www.ks.uiuc.edu/~johns/
>> 11.http://www.ks.uiuc.edu/Research/vmd/