From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 09 2015 - 15:32:56 CST

Vlastimil,
  I expect that you'll have the same issue with the Tk fonts with
VMD 1.9.2 since nothing changed in the VMD internals or Tcl/Tk versions
used therein. I'm going to start building a Tcl/Tk 8.6.x based version
of VMD in the next few weeks, so I hope to revisit some of this then.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 03, 2015 at 09:03:39AM +0100, Vlastimil Zma wrote:
> Hi John,
>
> I finally made time to test VMD 1.9.1 with TCL/TK 8.6 and it didn't help
> either.
>
> I noticed VMD 1.9.2 is out, so I will try that and let you know.
>
> Vlastimil
> 2014-08-13 19:28 GMT+02:00 John Stone <[1]johns_at_ks.uiuc.edu>:
>
> Vlastimil,
> Just FYI, the Tcl 8.5.0 version listed in the dependencies below
> is pretty archaic. The VMD builds we ship are based on at least
> Tcl 8.5.6 / 8.5.9, and we are now transitioning to Tcl 8.6.x. I would
> suggest
> not using the dependencies provided by debian if they are such old
> versions of Tcl/Tk.
>
> If we were to track down the source of your font problem
> to be a bug in Tcl/Tk itself, there would be no point in submitting
> a bug report on such an old version of Tcl/Tk, we would want to be using
> one
> of the last versions of the 8.5.x series, or one of the current 8.6.x
> releases in order to convince the Tcl/Tk developers to make/apply a fix.
>
> If the problem isn't Tcl/Tk itself, but rather something to do with
> the behavior of the X server of the font system on the affected machine,
> then this may not be important, but I wanted to mention that 8.5.0 is
> quite old and we began using later versions due to other known bugs
> that were in 8.5.0.
>
> Cheers,
> John Stone
> [2]vmd_at_ks.uiuc.edu
> On Wed, Aug 13, 2014 at 07:21:12PM +0200, Vlastimil Zma wrote:
> > Yet another build on debian wheezy, but on different machine. Not
> to build
> > a package.
> >
> > === Build dependencies ===
> > latex2html 2008-debian1-7
> > libfltk1.3-dev 1.3.0-8
> > libglu1-mesa-dev 8.0.5-4+deb7u2
> > libnetcdf-dev 1:4.1.3-6+b1
> > libxi-dev 2:1.6.1-1+deb7u1
> > make 3.81-8.2
> > python-dev 2.7.3-4+deb7u1
> > python-numpy 1:1.6.2-1.2
> > tcl-dev 8.5.0-2.1
> > texlive-latex-base 2012.20120611-5
> > tk-dev 8.5.0-2.1
> >
> > === Build process ===
> > tar -xzf vmd_1.9.1.orig.tar.gz
> > cd vmd-1.9.1
> > mv ../plugins plugins_src
> > export PLUGINDIR=$PWD/plugins
> > export TCL_INCLUDE_DIR=/usr/include/tcl
> > export TK_INCLUDE_DIR=/usr/include/tk
> > export PYTHON_INCLUDE_DIR=/usr/include/python2.7
> > export NUMPY_INCLUDE_DIR=/usr/include/python2.7/numpy
> > export VMDINSTALLBINDIR=$PWD/root/bin
> > export VMDINSTALLLIBRARYDIR=$PWD/root/lib
> > # Compile plugins
> > make -C plugins_src LINUXAMD64 TCLINC=-I${TCL_INCLUDE_DIR}
> > TCLLIB=-I/usr/share/tcltk/tcl8.5
> > make -C plugins_src distrib
> > sed -i 's|python2.5|python2.7|' configure
> > ./configure LINUXAMD64 OPENGL FLTK TK IMD XINPUT NETCDF CONTRIB
> TCL PYTHON
> > PTHREADS NUMPY NOSTATICPLUGINS
> > make -C src
> > make -C src install
> >
> > And it's broken again.
> >
> > Vlastimil
> >
> > 2014-08-13 18:34 GMT+02:00 Vlastimil ZAma
> <[1][3]zima_at_karlov.mff.cuni.cz>:
> >
> > Hi Josh,
> >
> > thanks for the reply. I've tried to build VMD as is quite some
> time ago,
> > but as far as I can remember I had the same issue. The paths
> doesn't
> > seem to be an issue, as I've defined all Tcl related
> variables,
> > otherwise the compilation would break. In my experience debian
> builds
> > complain quite effectively. Anyway I checked (grep -i
> 'error\|fail') the
> > output and haven't found any errors in there.
> >
> > I'll try to build VMD without packaging and provide further
> info.
> >
> > Vlastimil
> >
> > 2014-08-13 16:48 GMT+02:00 Josh Vermaas
> <[2][4]vermaas2_at_illinois.edu>:
> >
> > Hi Vlastimil,
> >
> > I've compiled VMD for Ubuntu and packaged it for myself as
> you've
> > done, and that isn't something I've seen before. Others
> have noticed
> > that depending on your linux installation, some characters
> are missing
> > from the system defaults (Angstrom seems to be the most
> common one).
> > Have you tried to build VMD in a non-packaged way first?
> Looking at
> > the rules file, the set directories look plausible
> depending on your
> > system setup, but I vaguely remember for instance needing
> to specify a
> > version number to pick up the appropriate header files and
> shared
> > libraries (so /usr/include/tcl8.5 instead of
> /usr/include/tcl, and
> > actually specifying a TCL_LIBRARY_DIR since the shared
> object wasn't
> > in /usr/lib). The debian package building process in my
> limited
> > experience hides errors very effectively, so if something
> went wrong,
> > it won't stop dpkg from building and making something that
> looks
> > plausible as a package that is totally broken.
> >
> > I'm just spitballing here. There is nothing obviously wrong
> (to my
> > eyes at least) with your configuration, and I've never seen
> the error
> > that you report, so I'm sorry I can't be more helpful. :(
> > -Josh Vermaas
> >
> > On 8/13/14, 5:12 AM, Vlastimil ZAma wrote:
> >
> > Hi everyone,
> >
> > continuing on this issue as there is indication I'm not
> the only one
> > suffering by this problem, see
> >
> [3][5]http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21361.html.
> >
> > Sum up the configuration:
> > A * Debian wheezy (stable), using system libraries, so
> they're not
> > likely to be broken.
> > A * I run VMD from console on my machine.
> > A * Doesn't look like problem with font installation.
> "font
> > families" returns the same result for tcl shell and vmd
> tcl shell.
> > A * I don't have SCIM installed which may cause
> troubles.
> > A * All my machines run under English locales
> "en_US.UTF-8".
> >
> > Since first error is
> >
> > X_QueryColors: BadValue (integer parameter out of range
> for
> > operation) 0xff000000
> >
> > I begin to suspect it may not be a problem related to
> fonts but
> > rather to the graphics in more general manner, e.g.
> wrong order of
> > layers.
> >
> > I tried to debug Tcl a bit and find out the errors
> appears after
> > function `::timeline::startTimeline` is finished. But
> this may be of
> > course caused by delay between window setup and its
> rendering.
> >
> > I've published debian packaging metadata at github
> > [4][6]https://github.com/ziima/vmd-debian. I'd be glad
> if anyone cares
> > to investigate or build the package using my metadata.
> > Alternatively I'm looking for somebody who compiled VMD
> successfully
> > on Debian or Ubuntu.
> >
> > Regards,
> > Vlastimil
> >
> > 2013-12-04 10:11 GMT+01:00 Vlastimil ZAma
> > <[5][7]zima_at_karlov.mff.cuni.cz>:
> >
> > Hi John,
> >
> > I haven't compiled Tk myself, I use system library.
> But all code
> > which is based on Tk works to my knowledge.
> >
> > As noted in my first email, I created a simple script
> based on
> > code I considered to cause problems in Timeline
> plugin:
> >
> > $ cat tk_test.tcl
> > package require Tk
> > font create tkFixedTimeline -family Courier -size -12
> > ttk::label .l -text "Attention!" -font
> tkFixedTimeline
> > grid .l -row 0
> >
> > This script works as expected. I also use a program
> Seaview, which
> > uses libfltk1.3 as well, without any problems. For
> these reasons I
> > expect that the system Tcl/Tk libraries work as they
> should.
> >
> > I was not able to find any other problematic code in
> Timeline
> > plugin and I'm not able to run the Timeline plugin
> outside of VMD,
> > so I don't have any other Tk GUI script to test. If
> you can
> > recommend any tests I'd like to try them out.
> > Vlastimil
> > 2013/11/27 John Stone <[6][8]johns_at_ks.uiuc.edu>
> >
> > Vlastimil,
> > A If your compilation of Tk is misbehaving, but
> our
> > pre-compiled VMD
> > binaries work okay, I would check what options
> were used when
> > you
> > compiled your Tk, and consider disabling
> antialiased fonts and
> > see if
> > that makes any difference. A Are you able to run
> an Tk scripts
> > with
> > just the Tcl/Tk builds you did on your machine? A
> In other
> > words, is
> > the problem isolated to Tcl/Tk on your machine, or
> do you have a
> > Tk GUI script that works in 'wishx' but fails
> within VMD? A It
> > would be
> > useful to narrow down the problem and see if it is
> purely an
> > issue
> > with your Tcl/Tk, or if it is something unique to
> running within
> > VMD.
> >
> > Cheers,
> > A John Stone
> > A [7][9]vmd_at_ks.uiuc.edu
> > On Wed, Nov 27, 2013 at 05:11:34PM +0100,
> Vlastimil ZAma wrote:
> > > A A Hi everybody,
> > >
> > > A A wheezy became stable, but I still
> experience this
> > problem.
> > >
> > > A A Anyway, I now suggests this may not be a
> problem of
> > fonts, but rather
> > > A A colors. I tried to check the error output,
> see my
> > previous post
> > > A
> > A
> [8][10]http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19942.html
> > and I
> > > A A have an impression that fonts might be
> properly rendered
> > but they are over
> > > A A painted by some other invalid entity
> (images or colored
> > blocks).
> > >
> > > A A Is there any other Tk-related
> build/runtime dependency
> > that is not mention
> > > A A in documentation?
> > >
> > > A A Regards,
> > > A A Vlastimil
> > >
> > > A A 2012/10/5 Vlastimil ZAma
> <[9][11]zima_at_karlov.mff.cuni.cz>
> > >
> > > A A A Hi,
> > >
> > > A A A when I compared my compiled VMD with
> precompiled
> > binary some time ago,
> > > A A A the fonts were present in the
> precompiled one. That is
> > why I expect
> > > A A A problems in compilation. I also did
> not noticed any
> > lack of fonts in
> > > A A A system paths, but I do not know which
> fonts to look
> > for.
> > >
> > > A A A > tclsh
> > > A A A % package require Tk
> > > A A A 8.5.11
> > > A A A % puts "$tcl_version"
> > > A A A 8.5
> > > A A A % puts "$tk_version"
> > > A A A 8.5
> > >
> > > A A A All tcl and tk packages I have are for
> amd64 bit
> > architecture (all
> > > A A A libraries are in /usr/lib).
> Specifically
> > >
> > > A A A
> [10][12]http://packages.debian.org/wheezy/tcl8.5 version
> > 8.5.11-2
> > > A A A
> [11][13]http://packages.debian.org/wheezy/tk8.5 version
> > 8.5.11-2
> > >
> > > A A A Regards,
> > > A A A Vlastimil
> > >
> > > A A A On 10/05/2012 04:08 PM, John Stone
> wrote:
> > >
> > > A A A A Hi,
> > > A A A A A A A Problems with Tk fonts are
> generally caused
> > not by the
> > > A A A A compilation of
> > > A A A A VMD (or FLTK) but are usually the
> result of a lack
> > of fonts installed
> > > A A A A with the X11 Windowing system. A
> Tk obtains its
> > fonts by querying the
> > > A A A A host windowing system for fonts
> that match the
> > characteristics of a
> > > A A A A request.
> > > A A A A If the host windowing system has
> no match, then Tk
> > tries to fallback
> > > A A A A to
> > > A A A A some font that is available.
> > >
> > > A A A A A From the description below, it
> sounds to me like
> > there might be
> > > A A A A something
> > > A A A A amiss the X11 window system fonts
> or one of the X11
> > libraries on the
> > > A A A A machine
> > > A A A A you're using, and that this is
> preventing the Tk
> > library embedded in
> > > A A A A VMD from getting anything other
> than the default
> > font.
> > >
> > > A A A A Since you're able to get a simple
> test to work in a
> > standalone
> > > A A A A interpreter,
> > > A A A A one thing that may be worth
> checking is whether
> > there might be some
> > > A A A A problem with the 64-bit libs on
> your machine. A Is
> > the "tclsh" that
> > > A A A A you
> > > A A A A run in your example below a 32-bit
> or 64-bit
> > library? A What do you
> > > A A A A get
> > > A A A A from this command, when you run it
> in your tclsh:
> > > A A A A A A A puts "$tcl_version"
> > > A A A A A A A puts "$tk_version"
> > >
> > > A A A A Cheers,
> > > A A A A A A A John Stone
> > > A A A A A A A [12][14]vmd_at_ks.uiuc.edu
> > >
> > > A A A A On Thu, Oct 04, 2012 at 11:07:03AM
> +0200, Vlastimil
> > ZAma wrote:
> > >
> > > A A A A A A A A A Hi,
> > >
> > > A A A A A A A A A after several attempts
> I still can not
> > resolve troubles with
> > > A A A A A tk fonts when
> > > A A A A A A A A A I compile VMD.
> > >
> > > A A A A A A A A A I am using 64bit
> Debian with following
> > vmd configuration:
> > >
> > > A A A A A A A A A ./configure LINUXAMD64
> OPENGL FLTK TK
> > IMD XINPUT NETCDF
> > > A A A A A CONTRIB TCL PYTHON
> > > A A A A A A A A A PTHREADS NUMPY
> NOSTATICPLUGINS
> > >
> > > A A A A A A A A A and tk packages:
> > > A A A A A A A A A libfltk1.3-dev 1.3.0-8
> (I also tried
> > fltk1.1)
> > > A A A A A A A A A tcl-dev 8.5.0-2
> > > A A A A A A A A A tk-dev 8.5.0-2
> > >
> > > A A A A A A A A A Still timeline,
> sequence viewer and
> > other plugins which uses
> > > A A A A A customized
> > > A A A A A A A A A fonts has invisible
> texts. I tried
> > anything I found on this
> > > A A A A A mailing list,
> > > A A A A A A A A A including LC_ALL=C in
> environment and
> > $HOME/.tkconrc file. I
> > > A A A A A also tried a
> > > A A A A A A A A A simple script with
> uses custom font
> > based on code of timeline
> > > A A A A A which works:
> > >
> > > A A A A A A A A A > A tclsh
> > > A A A A A A A A A package require Tk
> > > A A A A A A A A A font create
> tkFixedTimeline -family
> > Courier -size -12
> > > A A A A A A A A A ttk::label .l -text
> "Attention!" -font
> > tkFixedTimeline
> > > A A A A A A A A A grid .l -row 0
> > >
> > > A A A A A A A A A This shows nice small
> box with monofont
> > "Attention!" in it.
> > >
> > > A A A A A A A A A I will be glad for any
> help which would
> > help to resolve this
> > > A A A A A problem.
> > > A A A A A A A A A Vlastimil
> > --
> > NIH Center for Macromolecular Modeling and
> Bioinformatics
> > Beckman Institute for Advanced Science and
> Technology
> > University of Illinois, 405 N. Mathews Ave,
> Urbana, IL 61801
> > [13][15]http://www.ks.uiuc.edu/~johns/ A A A
> A A Phone:
> > 217-244-3349
> > [14][16]http://www.ks.uiuc.edu/Research/vmd/
> >
> > References
> >
> > Visible links
> > 1. mailto:[17]zima_at_karlov.mff.cuni.cz
> > 2. mailto:[18]vermaas2_at_illinois.edu
> > 3.
> [19]http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21361.html
> > 4. [20]https://github.com/ziima/vmd-debian
> > 5. mailto:[21]zima_at_karlov.mff.cuni.cz
> > 6. mailto:[22]johns_at_ks.uiuc.edu
> > 7. mailto:[23]vmd_at_ks.uiuc.edu
> > 8.
> [24]http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19942.html
> > 9. mailto:[25]zima_at_karlov.mff.cuni.cz
> > 10. [26]http://packages.debian.org/wheezy/tcl8.5
> > 11. [27]http://packages.debian.org/wheezy/tk8.5
> > 12. mailto:[28]vmd_at_ks.uiuc.edu
> > 13. [29]http://www.ks.uiuc.edu/%7Ejohns/
> > 14. [30]http://www.ks.uiuc.edu/Research/vmd/
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [31]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [32]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. mailto:zima_at_karlov.mff.cuni.cz
> 4. mailto:vermaas2_at_illinois.edu
> 5. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21361.html
> 6. https://github.com/ziima/vmd-debian
> 7. mailto:zima_at_karlov.mff.cuni.cz
> 8. mailto:johns_at_ks.uiuc.edu
> 9. mailto:vmd_at_ks.uiuc.edu
> 10. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19942.html
> 11. mailto:zima_at_karlov.mff.cuni.cz
> 12. http://packages.debian.org/wheezy/tcl8.5
> 13. http://packages.debian.org/wheezy/tk8.5
> 14. mailto:vmd_at_ks.uiuc.edu
> 15. http://www.ks.uiuc.edu/~johns/
> 16. http://www.ks.uiuc.edu/Research/vmd/
> 17. mailto:zima_at_karlov.mff.cuni.cz
> 18. mailto:vermaas2_at_illinois.edu
> 19. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21361.html
> 20. https://github.com/ziima/vmd-debian
> 21. mailto:zima_at_karlov.mff.cuni.cz
> 22. mailto:johns_at_ks.uiuc.edu
> 23. mailto:vmd_at_ks.uiuc.edu
> 24. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19942.html
> 25. mailto:zima_at_karlov.mff.cuni.cz
> 26. http://packages.debian.org/wheezy/tcl8.5
> 27. http://packages.debian.org/wheezy/tk8.5
> 28. mailto:vmd_at_ks.uiuc.edu
> 29. http://www.ks.uiuc.edu/%7Ejohns/
> 30. http://www.ks.uiuc.edu/Research/vmd/
> 31. http://www.ks.uiuc.edu/~johns/
> 32. http://www.ks.uiuc.edu/Research/vmd/

-- 
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/