VMD-L Mailing List

From: Stefan Boresch (stefan_at_mdy.univie.ac.at)
Date: Tue Nov 29 2016 - 02:20:31 CST

Joao,

thank you for the quick reply; unfortunately, I saw it only once I
was not at my desktop anymore, hence the late reply.

In reverse order: No "fn" key here, and the Windows key doesn't work
either. However, first pressing/holding either "Alt" key, then clicking
in the field forces the dropdown menu to appear.

I am not sure what "desktop effects" in my context mean. I am
running gnome 3.14, i.e., the default gnome 3 under Debian 8 ("jessie").
This runs in regular gnome 3 mode (i.e., not classic shell, as
I believe RHEL/Centos 7.x do). Obviously, there are some 'fancy effects',
but as opposed to KDE/Plasma, I wouldn't know that I can turn them off/on
in gnome3. Also, the same 'effects' are there in my main account and
in the secondary one. The one difference that I can think of is that
in my main account I made some configuration changes with gnome-tweak-tool
(focus follows mouse, minimization/maximation buttons on windows are the
main customizations that spring to mind).

The other difference between the two accounts is that the secondary
account was set up when I installed the machine, and it is left at
essentially default settings. The main account lives in a NFS mounted
home directory that goes back almost 20 years, so considerable cruft
has accumulated in its configuration (hidden .*) files, which probably
is impossible to sort out ..

If you can think of things to test / help debug this, let me know!
I'll get some other users (with varying degrees of gnome 3 customization)
to try ..

Thanks again for your help!

Best,

Stefan Boresch

On Mon, Nov 28, 2016 at 01:40:33PM +0000, João Ribeiro KS wrote:
> Hi Stefan,
>
> Can you please check if you have the desktop effects switched on in your
> main account? I saw the dropdown menus failing on some Linux builds because
> of these effects, but QwikMD resumed its normal behavior when these same
> effects were switched off. Also, using the function key "fn" or Windows key
> on the keyboard while selecting the the table cell, forces the dropdown
> menu to open.
>
> Thank you for your information
>
> Joao Ribeiro
>
> On Mon, Nov 28, 2016 at 6:32 AM Stefan Boresch <stefan_at_mdy.univie.ac.at>
> wrote:
>
> > Some more info ...
> >
> > I retried (on the same machine) with another (mostly virgin) account,
> > and there the dropdown boxes work.
> >
> > Thus, it seems that some 'cruft' in one of the zillion '.*' files of
> > my main account interfere with the correct operation of the
> > interface. I already (temporarily) disabled my .bashrc/.profile files,
> > as well as .vmdrc (which works around the stupid /usr/temp issue), but
> > no success.
> >
> > The only other difference between the two accounts is that the working
> > one has a local home directory, whereas the failing one has a NFS mounted
> > /home dir ..
> >
> > Helpful pointers appreciated, thanks!
> >
> > Stefan
> >
> >
> > On Mon, Nov 28, 2016 at 11:35:31AM +0100, Stefan Boresch wrote:
> > > Hi,
> > >
> > > hope this is the right place to ask. I just installed
> > > vmd 1.9.3beta4 specifically to test QwikMD and try to work my way
> > > through tutorial 1 (HIV Protease, M36I mutant).
> > >
> > > The first problem arises in step 5 (turning off the visual representation
> > > of waters). I don't get the dropdown menu; instead, when hoovering over
> > > 'VDW' or trying to click there, the cursor changes to a pencil (or
> > something
> > > looking like a pencil). However, trying to type has no effect. So, that's
> > > not too grave.
> > >
> > > Interestingly, the dropdown window appears as announced for renaming
> > > ACT to acecate (step 10).
> > >
> > > However, when attempting the mutation of MET36, the same problem arises.
> > > When clicking on Met36 the line is highlighted in light-blue, but instead
> > > of the dropdown window shown in the tutorial (step 15/16), I get again
> > the
> > > changed pencil-like cursor.
> > >
> > > Is anyone else seeing this?
> > >
> > > The machine is running Debian 8 ('jessie'), with all updates
> > > installed. I looked a bit in the vmd console window, but I see no
> > > messages / errors. Several volume calculations are carried out, but I
> > > assume this is for the structure checks ..
> > >
> > > Sincerely,
> > >
> > > Stefan Boresch
> > >
> > > PS: The vmd I installed is the one precompiled for AMD64/CUDA
> > 7.5/OptiX/..
> > > I presently don't have cuda 7.5 on that machine, so no cuda device is
> > > found and obviously there is no OptiX functionality. All standard
> > > functionality of VMD, however, seems to work fine, so I doubt that
> > > this has anything to do with the QwikMD problems.
> > >
> >
> >