VMD-L Mailing List
From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Aug 29 2018 - 15:06:07 CDT
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Hi John,
ContactMap = Unusable
Timeline = Unusable
I've systematically worked through the other GUI-accessible plugins, and none of them show the same behavior. I've attached a screenshot of what the panel looks like for me. No text is displayed whatsoever, except for a few stray underscores where text ought to be.
-Josh
On 2018-08-29 11:04:50-06:00 John Stone wrote:
Hi,
My guess here is that there is some sort of issue with Tk fonts breaking things
on your respective builds. You can see that Timeline uses "-font $monoFont" on a
large number of its GUI widgets, and it assigns the $monoFont variable as follows:
font create tkFixedTimeline -family Courier -size -12
set monoFont tkFixedTimeline
I see that in the Contact Map plugin, it is not creating a new font instance,
and is currently just using "tkFixed", which one would expect to work out-of-the-box:
set monoFont tkFixed
Looking at the contact map plugin, it is doing exactly the same thing, and I find
similar, but not necessarily identical code in the following plugins (complete list):
aligntool
atomedit
contactmap
heatmapper
multiplot
multiseqdialog
nmwiz
paratool
phylotree
plumed
symmetrytool
timeline
vmdtkcon
Can you guys look a few of these specific plugins and see if they exhibit the
same issues, and perhaps give examples of one or two that don't exhibit the problem
just as a point of comparison?
Best,
John
On Wed, Aug 29, 2018 at 04:11:13PM +0000, Vermaas, Joshua wrote:
> Hi Peter,
>
> Now that you mention it, you are right! In my own compiled builds, these
> plugins are also broken. My advice was based on past experience with the
> "clone representations" and ruler plugins I use with some regularity,
> which didn't work with 8.6. I never tried using timeline or the contact
> map plugins, likely because they were broken in my install, and my own
> workflows were pretty much set before the plugins were released. Sorry for
> sending you down the wrong path. :(
>
> In terms of them getting fixed, I'd say the likelihood is pretty high, as
> the author of the plugins is still at UIUC from what I understand.
> However, it clearly works for them, so I'm not sure what is wrong, since
> the graphical window is all drawn via Tcl...
>
> -Josh
>
>
>
> On 2018-08-29 09:15:29-06:00 Peter Kroon wrote:
>
> And to follow up, I recompiled vmd with TCL/TK 8.5, and they still don't
> work :'(
>
> I confirmed that I have version 8.5 by writing 'puts $tcl_version' in
> the console.
>
>
> Peter
>
>
> On 29-08-18 17:04, Peter Kroon wrote:
> > Hi Josh,
> >
> >
> > thanks for the swift reply. Is there any hope that those will be updated
> > somewhere in the future, or should they be considered unmaintained and
> > deprecated?
> >
> >
> > Peter
> >
> >
> > On 28-08-18 14:21, Vermaas, Joshua wrote:
> >> Hi Peter,
> >>
> >> Some of the plugins are picky, and require Tcl 8.5. If you use 8.6
> >> with them, some of the commands used to draw the windows break, and
> >> you get the blank displays you've encountered.
> >>
> >> -Josh
> >>
> >>
> >>
> >> On 2018-08-28 04:54:52-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:
> >>
> >> Hi all,
> >>
> >> I have a home-compiled version of VMD 1.9.3, and some plugins (e.g.
> >> contact map and timeline) don't show any text in their interface
> >> windows. There are (were?) more messages on this list with the same
> >> issue, but no solutions other than using the precompiled binaries. I
> >> compiled my VMD and plugins with the system TCL 8.6.
> >>
> >> The console spews the following errors:
> >>
> >> vmd > X_QueryColors: BadValue (integer parameter out of range for
> >> operation) 0xff000000
> >> XRequest.139: BadMatch (invalid parameter attributes) 0x184
> >> XRequest.139: RenderBadPicture (invalid Picture parameter) 0x6800063
> >> XRequest.139: BadMatch (invalid parameter attributes) 0x184
> >> XRequest.139: RenderBadPicture (invalid Picture parameter) 0x6800067
> >> XRequest.139: BadMatch (invalid parameter attributes) 0x184
> >> XRequest.139: RenderBadPicture (invalid Picture parameter) 0x6800069
> >> XRequest.139: BadMatch (invalid parameter attributes) 0x184
> >> XRequest.139: RenderBadPicture (invalid Picture parameter) 0x6800082
> >>
> >> etc...
> >>
> >> Does anyone have any blinding insight in how I can further debug or fix
> >> this?
> >>
> >>
> >> Peter
> >>
> >>
> >
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 https://na01.safelinks.protection.outlook.com/?url=http:%2F%2Fwww.ks.uiuc.edu%2F~johns%2F&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cc3c2e1c1e13e4f1f072a08d60dd186df%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636711590897327618&sdata=7EhXXHzds3cZxWOG2Bxib3G7DqEs4ZSFEz0UmgdtleM%3D&reserved=0 Phone: 217-244-3349 https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fvmd%2F&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cc3c2e1c1e13e4f1f072a08d60dd186df%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636711590897327618&sdata=HQLZN%2Fj4JLbuIorae8LAvg8qE9KwD1UMIs9TEUtDebo%3D&reserved=0
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