VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 10 2021 - 15:47:29 CDT

Chris,
  If you run more recent versions of VMD 1.9.4, the issue with pack vs. grid
should already be fixed for the multimolanim plugin (or at least that's my
knee jerk recollection). I'm up to my eyeballs with work dealing with a
VMD funding proposal, but check the newer builds and let me know if you
still have the pack vs. grid issue.

Best regards,
  John Stone

On Thu, Jun 10, 2021 at 12:51:13PM -0600, Chris Neale wrote:
> 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.
> > 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/