VMD-L Mailing List

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Sat Oct 30 2010 - 12:47:22 CDT

Hi Christian,

You can also try playing with the Volmap plugin. It is fairly
flexible, so it might be able to do exactly what you want.

Best,
Jerome

2010/10/29 Ajasja LjubetiÄ <ajasja.ljubetic_at_gmail.com>:
> Hi,
> set sel [atomselect top "z>-1 and z <1"]
> $sel get {x y}
> will select everything lying in the xy plane betwen z>-1 and z<1 and output
> the x y coordinates.
> when designing a new selection it is most useful to create a new
> representation and enter the selection there, so one can see exactly which
> atoms are selected.
> Regards,
> Ajasja
>
> 2010/10/29 Christian Jorgensen <christian.jorgensen_at_merton.ox.ac.uk>
>>
>> Hi all,
>> I am trying to write a Tcl script for calculating the xy-plane of my
>> molecules in the solvent box as given in the trajectory, dcd, output file. I
>> want to know the coordinates of the molecule(s) in the xy-plane, and then I
>> want to map this number density distribution of all atoms of the trajectory
>> onto the z-axis to create a slice of volume
>> xyΔz
>>
>> Question: Does anyone know a command in Tcl to make a selection (when the
>> .tcl script is source in VMD) to select a flat xy-region and output the
>> coordinates?
>>
>> Any help would be most appreciated!
>> christian
>
>