From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Oct 09 2013 - 15:51:15 CDT

On Wed, Oct 9, 2013 at 10:44 PM, Chris Knorowski <cdknorow_at_iastate.edu> wrote:
> Thanks Axel,
>
> The problem is I am rotating the screen, the planes that I would like to cut
> are not necessarily in the x,y,z direction. Using the clipping tool you can
> set it so that the normal to view is clipped but it is just not very easy to
> line up correctly. Its much easier to line it up so that the plane I want to
> clip is perpendicular to the view (in orthographic). I can calculate the
> vector to clip but it isn't straightforward to do, especially when I want to
> do it on a lot of differently oriented crystals. I guess I'm asking if there
> is a command that outputs what the current north, south or east vector in
> the display window is.

have you seen the "Normal follows view" option? i usually play with
enabling/disabling that and get what i need quite easily. i also do
the rotations from the command line, to make it easy to undo them. and
then once the clipping planes are set up as i want, i rotate the viz
into the final and desire position.

as for your final remark/question. it has to be somewhere in one of
these matrices that are used by the save_state command/script:
molinfo $mol get {center_matrix rotate_matrix scale_matrix global_matrix}

the user's guide hopefully has the details to tell you what has what you need.

axel.

>
> Thanks,
> Chris
>
>
> On Wed, Oct 9, 2013 at 3:19 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Wed, Oct 9, 2013 at 9:25 PM, Chris Knorowski <cdknorow_at_iastate.edu>
>> wrote:
>> > Dear all,
>> >
>> > I have a quick question about vmd. I am using the clip tool to aid in
>> > visualizations of crystal structures. I'm wondering if there is a quick
>> > way
>> > to figure out what direction in vmd the image is oriented so I can plug
>> > that
>> > into the clip tool. For example, I'd like to be able to clip the plane
>> > whose normal is straight up (not the normal to the view).
>>
>> Display->Axes
>>
>> if you don't rotate. x is to the right, y is up and z is toward you.
>>
>> axel.
>>
>> >
>> > Thanks,
>> > Chris
>> >
>> >
>> > --
>> > Christopher Knorowski
>> >
>> > Iowa State Physics Department
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
>
> --
> Christopher Knorowski
>
> Iowa State Physics Department

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.