From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 12 2021 - 00:46:06 CST

Hi,
  FYI, I believe we've tracked down the likely source of this issue
in the version of the Tcl/Tk "Tablelist" widget the VMD plugins have
been using, and we are working toward a resolution.

Best,
  John

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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-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/