VMD-L Mailing List

From: Jennifer Williams (Jennifer.Williams_at_ed.ac.uk)
Date: Wed May 11 2011 - 06:32:13 CDT

Hi,

Apologies if this is a trivial question.

I have a cubic molecule (.xyz file) and I simply want to take a slice
through it. i.e as if to cut it in half and display the face of the
cut-edge.

Reading through the documentaion I thought the mol volume tool might
do the trick but I can't seem to get the command right. I thought the
command was the following...

mol volume top {0 0 0} {1 0 0}

with the first set of brackets denoting whether I would be cutting
parallel to the x, y or z axis and the second denoting how far along
the cartesian axis of the molecule I would be cutting (or vice versa
-can't tell at the moment).

so for example if I wanted to slice the molecule at the midpoint
parallel to teh x axis, I supposed the command would be:

mol volume top {1 0 0} {0 0.5 0}

could someone please give the correct command to do this?

Thanks

Jenny
Could someone please

Quoting Jennifer Williams <Jennifer.Williams_at_ed.ac.uk> on Thu, 27 May
2010 16:21:49 +0100:

>
>
> Hi,
>
> I have a cif file of a metal organic framework. There is water
> coordinated but the XRD generated cif files only has the positions
> of the oxygens, not the hydrogens.
>
> Can someone recommend a *free* software which can do a hydrogen
> adjust and then a minimisation/optimisation to find the positions of
> these hydrogens whilst keeping all the known atoms fixed? Can VMD do
> this? I know Materials Studio can do this but I don't have access to
> this.
>
> Thanks
>
> Jenny
>
>
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>
>

Dr. Jennifer Williams
Institute for Materials and Processes
School of Engineering
University of Edinburgh
Sanderson Building
The King's Buildings
Mayfield Road
Edinburgh, EH9 3JL, United Kingdom
Phone: ++44 (0)131 650 4 861 

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.