VMD-L Mailing List

From: Abolfazl Musavi (ab.musavi1990_at_gmail.com)
Date: Wed Jun 05 2019 - 11:46:01 CDT

Thank you dear Axel.

On Mon, 3 Jun 2019 at 05:51, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

>
>
> On Sat, Jun 1, 2019 at 11:28 PM Abolfazl Musavi <ab.musavi1990_at_gmail.com>
> wrote:
>
>> Dear all,
>>
>>
>>
>> I want to draw several cubic boxes to separate different regions in the
>> simulation box. I want their sides to be semi-transparent and with
>> different colors. I do not want to draw a cube by lines because then there
>> will not be any side surfaces.
>>
>>
>>
>> I would be appreciated if anyone could tell how to do that in VMD.
>>
>
> the most straightforward way to do this is via VMD Tcl scripting. here is
> a quick demo. for the detailed syntax, please refer to the VMD User's Guide.
>
> # create demo coordinates file
> set fp [open "cube.xyz" "w"]
> puts $fp "8\ncube edges\nH -5.0 -5.0 -5.0\nH -5.0 -5.0 5.0\nH -5.0
> 5.0 -5.0\nH -5.0 5.0 5.0\nH 5.0 -5.0 -5.0\nH 5.0 -5.0 5.0\nH 5.0
> 5.0 -5.0\nH 5.0 5.0 5.0\n"
> close $fp
>
> # load file and visualize as points
> set mol [mol new cube.xyz waitfor all]
> mol modstyle 0 $mol Points 1.000000
>
> # draw three sides as transparent squares
> graphics $mol material Transparent
> graphics $mol color yellow
> graphics $mol triangle {-5 -5 -5} {-5 -5 5} {-5 5 -5}
> graphics $mol triangle {-5 5 5} {-5 -5 5} {-5 5 -5}
> graphics $mol color red
> graphics $mol triangle {-5 -5 -5} {5 -5 5} {5 -5 -5}
> graphics $mol triangle {-5 -5 5} {5 -5 5} {-5 -5 -5}
> graphics $mol color blue
> graphics $mol triangle {-5 5 5} {-5 -5 5} {5 -5 5}
> graphics $mol triangle {-5 5 5} { 5 5 5} {5 -5 5}
>
> good luck,
> axel.
>
>>
>>
>> Regards
>>
>> Abolfazl
>>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>