VMD-L Mailing List

From: Vlastimil Zíma (zima_at_karlov.mff.cuni.cz)
Date: Wed Aug 13 2014 - 04:12:10 CDT

Hi everyone,

continuing on this issue as there is indication I'm not the only one
suffering by this problem, see
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21361.html.

Sum up the configuration:
 * Debian wheezy (stable), using system libraries, so they're not likely to
be broken.
 * I run VMD from console on my machine.
 * Doesn't look like problem with font installation. "font families"
returns the same result for tcl shell and vmd tcl shell.
 * I don't have SCIM installed which may cause troubles.
 * 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
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 Zíma <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 <johns_at_ks.uiuc.edu>
>
>> Vlastimil,
>> 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. Are you able to run an Tk scripts with
>> just the Tcl/Tk builds you did on your machine? 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? 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,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Wed, Nov 27, 2013 at 05:11:34PM +0100, Vlastimil Zíma wrote:
>> > Hi everybody,
>> >
>> > wheezy became stable, but I still experience this problem.
>> >
>> > Anyway, I now suggests this may not be a problem of fonts, but rather
>> > colors. I tried to check the error output, see my previous post
>> > http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19942.html
>> and I
>> > have an impression that fonts might be properly rendered but they
>> are over
>> > painted by some other invalid entity (images or colored blocks).
>> >
>> > Is there any other Tk-related build/runtime dependency that is not
>> mention
>> > in documentation?
>> >
>> > Regards,
>> > Vlastimil
>> >
>> > 2012/10/5 Vlastimil ZAma <zima_at_karlov.mff.cuni.cz>
>> >
>> > Hi,
>> >
>> > when I compared my compiled VMD with precompiled binary some time
>> ago,
>> > the fonts were present in the precompiled one. That is why I expect
>> > problems in compilation. I also did not noticed any lack of fonts
>> in
>> > system paths, but I do not know which fonts to look for.
>> >
>> > > tclsh
>> > % package require Tk
>> > 8.5.11
>> > % puts "$tcl_version"
>> > 8.5
>> > % puts "$tk_version"
>> > 8.5
>> >
>> > All tcl and tk packages I have are for amd64 bit architecture (all
>> > libraries are in /usr/lib). Specifically
>> >
>> > http://packages.debian.org/wheezy/tcl8.5 version 8.5.11-2
>> > http://packages.debian.org/wheezy/tk8.5 version 8.5.11-2
>> >
>> > Regards,
>> > Vlastimil
>> >
>> > On 10/05/2012 04:08 PM, John Stone wrote:
>> >
>> > Hi,
>> > A A Problems with Tk fonts are generally caused not by the
>> > compilation of
>> > VMD (or FLTK) but are usually the result of a lack of fonts
>> installed
>> > with the X11 Windowing system. A Tk obtains its fonts by
>> querying the
>> > host windowing system for fonts that match the characteristics
>> of a
>> > request.
>> > If the host windowing system has no match, then Tk tries to
>> fallback
>> > to
>> > some font that is available.
>> >
>> > A From the description below, it sounds to me like there might be
>> > something
>> > amiss the X11 window system fonts or one of the X11 libraries on
>> the
>> > machine
>> > you're using, and that this is preventing the Tk library
>> embedded in
>> > VMD from getting anything other than the default font.
>> >
>> > Since you're able to get a simple test to work in a standalone
>> > interpreter,
>> > one thing that may be worth checking is whether there might be
>> some
>> > problem with the 64-bit libs on your machine. A Is the "tclsh"
>> that
>> > you
>> > run in your example below a 32-bit or 64-bit library? A What do
>> you
>> > get
>> > from this command, when you run it in your tclsh:
>> > A A puts "$tcl_version"
>> > A A puts "$tk_version"
>> >
>> > Cheers,
>> > A A John Stone
>> > A A vmd_at_ks.uiuc.edu
>> >
>> > On Thu, Oct 04, 2012 at 11:07:03AM +0200, Vlastimil ZAma wrote:
>> >
>> > A A Hi,
>> >
>> > A A after several attempts I still can not resolve troubles
>> with
>> > tk fonts when
>> > A A I compile VMD.
>> >
>> > A A I am using 64bit Debian with following vmd configuration:
>> >
>> > A A ./configure LINUXAMD64 OPENGL FLTK TK IMD XINPUT NETCDF
>> > CONTRIB TCL PYTHON
>> > A A PTHREADS NUMPY NOSTATICPLUGINS
>> >
>> > A A and tk packages:
>> > A A libfltk1.3-dev 1.3.0-8 (I also tried fltk1.1)
>> > A A tcl-dev 8.5.0-2
>> > A A tk-dev 8.5.0-2
>> >
>> > A A Still timeline, sequence viewer and other plugins which
>> uses
>> > customized
>> > A A fonts has invisible texts. I tried anything I found on
>> this
>> > mailing list,
>> > A A including LC_ALL=C in environment and $HOME/.tkconrc
>> file. I
>> > also tried a
>> > A A simple script with uses custom font based on code of
>> timeline
>> > which works:
>> >
>> > A A > A tclsh
>> > A A package require Tk
>> > A A font create tkFixedTimeline -family Courier -size -12
>> > A A ttk::label .l -text "Attention!" -font tkFixedTimeline
>> > A A grid .l -row 0
>> >
>> > A A This shows nice small box with monofont "Attention!" in
>> it.
>> >
>> > A A I will be glad for any help which would help to resolve
>> this
>> > problem.
>> > 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
>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> http://www.ks.uiuc.edu/Research/vmd/
>>
>
>