VMD-L Mailing List

From: Chris Neale (candrewn_at_gmail.com)
Date: Thu Jun 10 2021 - 18:58:54 CDT

Confirmed that 1.9.4a51 does not give me any errors.

Thank you again,
Chris.

On Thu, Jun 10, 2021 at 2:47 PM John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/
>