From: Pawel Kedzierski (
Date: Fri Oct 30 2020 - 14:54:21 CDT

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

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
>> < <>> 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>