VMD-L Mailing List

From: Chris Neale (candrewn_at_gmail.com)
Date: Thu Jun 10 2021 - 13:51:13 CDT

Oh yeah, that’s the sauce! Thanks Axel! This does precisely what I was
looking for.

For what it’s worth, I had to edit /Applications/VMD\
1.9.4a43-Catalina-Rev6.app/Contents/vmd/plugins/noarch/tcl/multimolanim1.0/multimolanim.tcl
to comment out all of the “pack” commands or else I got the error listed
below. I’m not sure if I’m even missing anything after that modification
since the resulting tool appears to be fully functional.

ERROR) Creation of window for 'multimolanim' failed (cannot use geometry
manager grid inside .molanimgui which already has slaves managed by pack).

I found a thread suggesting a similar problem might have been introduced in
a different tool by changes in tcl:
https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/27223.html

And more specific information was gleaned from here:
https://urldefense.com/v3/__https://stackoverflow.com/questions/23584325/cannot-use-geometry-manager-pack-inside__;!!DZ3fjg!sAL65M7A_28IPON8g_r0boFrtvs-7GQIkbLS9TJd1qNILIoiP0D1UG8sdN2goX0n3A$

Here’s my system:
Info) VMD for MACOSXX86_64, version 1.9.4a43 (June 11, 2020)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 16 CPUs detected.
Info) High-DPI OpenGL display support enabled.
Info) OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
Info) Features: STENCIL MDE MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (16384x16384), 3-D (16384x16384x16384), Multitexture
(8)

Changes I made:

$ diff multimolanim.tcl backup_original_multimolanim.tcl

122c122

< #pack $w.menubar -side top -padx 1 -fill x 

---
>     pack $w.menubar -side top -padx 1 -fill x
134c134
<     #pack $w.menubar.help -side right
---
>     pack $w.menubar.help -side right
139c139
<     #pack $f -side top -fill x
---
>     pack $f -side top -fill x
162,171c162,171
<     #pack $f.m -side left
<     #pack $f.ms -side left -fill x
<     #pack $f.s -side left
<     #pack $f.ss -side left -fill x
<     #pack $f.c -side left
<     #pack $f.cpb -side left -fill x
<     #pack $f.csb -side left -fill x
<     #pack $f.cst -side left -fill x
<     #pack $f.csf -side left -fill x
<     #pack $f.cpf -side left -fill x
---
>     pack $f.m -side left
>     pack $f.ms -side left -fill x
>     pack $f.s -side left
>     pack $f.ss -side left -fill x
>     pack $f.c -side left
>     pack $f.cpb -side left -fill x
>     pack $f.csb -side left -fill x
>     pack $f.cst -side left -fill x
>     pack $f.csf -side left -fill x
>     pack $f.cpf -side left -fill x
On Thu, Jun 10, 2021 at 12:26 PM Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
>
> On Thu, Jun 10, 2021 at 2:03 PM Chris Neale <candrewn_at_gmail.com> wrote:
> [...]
>
>>
>> My actual use case is something like docking, where I want to view a
>> "trajectory" with hundreds or thousands of frames that all have the same
>> protein target but each frame has a different chemical bound, possibly in a
>> different location, and certainly with different numbers/types of atoms in
>> the small molecule component. I want them in the same molecule because
>> activate/deactivate commands (or GUI) for different molecules is more
>> cumbersome than pushing the frame slider along (though this makes me
>> realize that just having a slider that activates/deactivates separate
>> molecules in turn would do what I need after cloning a representation).
>>
>
> Have you looked at these two plugins?
>
> https://www.ks.uiuc.edu/Research/vmd/plugins/multimolanim/
> https://www.ks.uiuc.edu/Research/vmd/plugins/clonerep/
>
> They have been part of VMD for a very long time... Although "thousands of
> frames" may be pushing the limit.
>
> Axel.
>
>
>> Thank you,
>> Chris.
>>
>
> --
> Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!sAL65M7A_28IPON8g_r0boFrtvs-7GQIkbLS9TJd1qNILIoiP0D1UG8sdN3VJaMeQA$ 
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>