From: Stefan Boresch (stefan_at_mdy.univie.ac.at)
Date: Tue Nov 29 2016 - 03:10:35 CST

Small follow-up: I 'borrowed' a new coworker's machine to test quikmd,
and there the dropdown menus do work. Hardware and Software of the
two machines in question are identical; this was also tried with
gnome3 (same version, same graphics driver). Thus, this really must be
some hidden 'cruft' in my config files ..

Let me use the opportunity to ask some more general questions about
the capabilities of qwikmd: (1) The tool will change protonation
states for me (e.g. GLU -> GLUP), but I must provide the
information, right? (E.g., from propKa ..) (2) If I have gaps in
a structure, it is again my responsibility to fix the PDB file (i.e.,
to provide the missing coordinates)? Can one coax ModelMaker into
"just" loop modelling?

I should explain that I am looking into QwikMD mostly for courses, as
it seems a gentler introduction to (setting up) MD (correctly)
compared to charmm-gui/charmm/namd ..

Thanks again, best regards,

Stefan Boresch

On Mon, Nov 28, 2016 at 01:40:33PM +0000, Joo 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.
> > >
> >
> >