VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed May 11 2011 - 09:16:40 CDT

hi jenny,

On Wed, May 11, 2011 at 7:32 AM, Jennifer Williams
<Jennifer.Williams_at_ed.ac.uk> wrote:
>
>
> 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).

i don't know which documentation you read, but it cannot be the
VMD documentation. the "mol volume" command can be used
to add a volumetric data set (i.e. a bunch of gridpoints to be used
for isosurfaces and alike) to your coordinate data, but not to cut out
a face. one way to do what you want would be to change atom selection
to make it some function of x, y, or z-coordinates of atoms.

for instance try something like "y < x" instead of "all" as selection.

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

if the molecule is centered at the origin you can try: "z < 0"

cheers,
    axel.
>
> 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.
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.