VMD-L Mailing List

From: Stefan Boresch (stefan_at_mdy.univie.ac.at)
Date: Mon Nov 28 2016 - 06:31:30 CST

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.
>