VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Nov 01 2020 - 01:43:46 CST

Hi Pawel, Mariano,
  I just tested the molefacture version in one of my recent test builds
and I saw exactly the same behavior that Pawel is reporting. The bug
is apparent in test versions that date back to February 2020, and I don't
think that any of the recent changes for QM Tool integration have any
impact on this AFAIK. The table cells never respond to the intended
editing mouse clicks, at least in my testing on Linux w/ a test build
using Tcl/Tk 8.6.x, and Pawel would be running test versions using
Tcl/Tk 8.5.x, so this does not appear to be something specific to
a particular Tcl/Tk version.

Best,
  John Stone

On Fri, Oct 30, 2020 at 08:54:21PM +0100, Pawel Kedzierski wrote:
> Dear Mariano,
> W dniu 30.10.2020 o 14:34, Spivak, Mariano Alejo pisze:
>
> Hi Pawel,
> The functionality you are looking for is indeed implemented in
> Molefacture 2.0.
> If you click on the cell that shows the pen icon, you should be able to
> edit that cell content.
> After you click, the cell is highlighted in white and a text cursor
> (vertical line) appears inside.
>
> I can select atoms from both the table and in the OpenGL window and I do
> see the pen icon when hovering over atom name, type etc. fields.
>
> However, I tried single & double clicks with left, middle and right
> buttons, but the cells are not highlighted in white and the cursor does
> not appear, there is just no effect apart from the green selection of the
> entire row.
>
> If you still have issues, please send me the details of your operating
> system and I will check it. Also you could try with the most recent
> alpha version of VMD 1.9.4.
>
> I have just downloaded and installed
> vmd-1.9.4a48.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185.opengl.tar.gz
>
> Tried this on three different systems: Ubuntu 16.04 LTS, Ubuntu 20.04.1
> LTS and Debian 10, everywhere I observe the same behaviour - same as with
> 1.9.4 alpha 38.
>
> I have checked "puts $tcl_version" from VMD cli and it returns 8.5.
>
> What else should I check?
>
> Thank you
>
> Best
>
> On Oct 30, 2020, at 7:17 AM, Pawel Kedzierski
> <[1]pawel.kedzierski_at_pwr.edu.pl> wrote:
>
> Dear VMD users,
>
> The new Molefacture 2.0 VMD plugin available at least from VMD version
> 1.9.4a38 is a surprise for me. I used Molefacture previously to
> prepare PDB and PSF files for parametrization with FFTK. However, the
> new version is missing the functionality which is necessary for this
> purpose. Specifically, I am unable to edit:
>
> * atom names
> * atom types
> * partial charges (to set constant 0.09 charge on HA hydrogens)
>
> Am I missing something? When I select a row in the table of atoms and
> hover the pointer, say, over the atom type, I see the pointer changing
> to a pen icon. It would suggest the ability to edit but I tried
> clicking all buttons and typing, nothing works. Tried on Linux.
>
> Could anyone suggest workarounds, or another tool able to start with a
> simple PDB file? I know I can manualy edit the PDB file, prepare the
> matching topology file and then use either autopsf or psfgen, but this
> workflow is more elaborate and error prone, and I need it for
> classes.
>
> With regards,
>
> Pawel
>
> <pawel_kedzierski.vcf>
>
> References
>
> Visible links
> 1. mailto:pawel.kedzierski_at_pwr.edu.pl

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