Hi Jason,
Unsetting static_singletons fixed this! Thanks a lot!
Nicolas
On Tue, Mar 8, 2011 at 11:55 AM, Jason Vertrees <
[email protected]> wrote:
> Hi Nicolas,
>
> unset static_singletons
>
> Cheers,
>
> -- Jason
>
> On Tue, Mar 8, 2011 at 10:21 AM, Nicolas Bigaouette
> <[email protected]> wrote:
> > Hi Jason,
> >
> > Thanks for your input.
> >
> > I've looked at the all_states option, but it was not set (or set to
> false).
> > If I explicitely set it to 1/true, I see every state of particles and
> boxes.
> >
> > To reproduce, I've created a small test script and uploaded it to github.
> > You can get it here:
> > https://github.com/nbigaouette/pymol_boxes
> > and clone it:
> > git clone git://github.com/nbigaouette/pymol_boxes.git
> > Then simply run with:
> > ./pymol_boxes.py
> >
> > Even though all information is located in the data files, I just plot box
> id
> > #121 for now. The white ball is traveling from right to left, and when it
> > leaves box #121, the box should disappear: it is not. If you disable the
> > check at line 44, all boxes will be drawn. The two smallest box appearing
> at
> > frame 22 of the animation disappear at frame 25. Box 121 is shown every
> > frame while it should disappear at frame 8.
> >
> > I think I've found the problem. If I add a box at frame 1 (the first
> one),
> > it will stay on forever! To verify this, I added a (commented) test at
> line
> > 43. If I skip t=0 (the first frame, note the t+1 send to
> > pymol_objects.DrawBox() at line 54), then box 121 will disappear when it
> > should (when the white particle is leaving it). If the box is added at
> the
> > first frame, it will stay there during the animation...
> >
> > Could that be a bug in pymol? Or is there still something I'm missing?
> >
> > I hope the example code will help out.
> >
> > Thanks a lot!
> >
> > Nicolas
> >
> >
> > On Mon, Mar 7, 2011 at 10:17 PM, Jason Vertrees
> > <[email protected]> wrote:
> >>
> >> Hi Nicolas,
> >>
> >> It sounds like you have the "all_states" option set. So, to only have
> >> one object state shown at a time, try
> >>
> >> unset all_states
> >>
> >> Also, deleting anything in PyMOL is easy:
> >>
> >> delete objName
> >>
> >> or through the cmd API:
> >>
> >> cmd.delete("objName")
> >>
> >> Cheers,
> >>
> >> -- Jason
> >>
> >> On Mon, Mar 7, 2011 at 9:11 PM, Nicolas Bigaouette
> >> <[email protected]> wrote:
> >> > Hi Jason,
> >> >
> >> > Thanks for your reply. No, I'm not deleting the cgo objects after the
> >> > relevant frames. Actualy, I don't know how. This what I wanted to do
> >> > though.
> >> >
> >> > I was able to achieve a workaround. Each time load_cgo() is called to
> >> > create
> >> > a box, a loop will go through all later time steps adding an empty cgo
> >> > object of the same name. But it seems to be really slow, as expected.
> >> >
> >> > So my error was thinking that giving an object a state would draw the
> >> > object
> >> > only at that frame: it seems it is drawn for all later frames.
> >> >
> >> > Thus, how can I add an object only for a given state/frame? Should I
> >> > delete
> >> > the object at the next state/frame? What would be the command to
> delete
> >> > a
> >> > cgo object?
> >> >
> >> > Should I store what load_cgo() returns and issue a "delete" over that
> >> > object?
> >> >
> >> > Thanks!
> >> >
> >> >
> >> > On Mon, Mar 7, 2011 at 9:03 PM, Jason Vertrees
> >> > <[email protected]> wrote:
> >> >>
> >> >> Hi Nicolas,
> >> >>
> >> >> Are you hiding or deleting the boxes after the relevant frame passes?
> >> >> This is hard to debug without seeing sample code.
> >> >>
> >> >> Cheers,
> >> >>
> >> >> -- Jason
> >> >>
> >> >> On Mon, Mar 7, 2011 at 8:39 PM, Nicolas Bigaouette
> >> >> <[email protected]> wrote:
> >> >> > Hi all,
> >> >> >
> >> >> > I'm usin pymol to vizualize my molecular dynamics code. Particle
> >> >> > positions
> >> >> > is saved in a single .xyz file. An example is:
> >> >> > 2
> >> >> > 0.00000 fs -- MD of 2 particles (position in Angstrom)
> >> >> > A 0.000 0.000 0.000
> >> >> > E 13.020 0.000 0.000
> >> >> > 2
> >> >> > 0.00050 fs -- MD of 2 particles (position in Angstrom)
> >> >> > A 0.000 0.000 0.000
> >> >> > E 10.520 0.000 0.000
> >> >> > [...]
> >> >> > The number "2" (appearing twice) gives the number of particles to
> be
> >> >> > read
> >> >> > for that time step.
> >> >> >
> >> >> > I want to add some boxes around some of the particles, so I wrote a
> a
> >> >> > function that creates a CGO object and add it to a frame/timestep
> >> >> > using
> >> >> > "cmd.load_cgo(my_cjo_obj,boxname,timestep)".
> >> >> >
> >> >> > For each time step of my simulation, I load the box informations
> from
> >> >> > a
> >> >> > file
> >> >> > and call my cgo-creating function for the boxes present in the
> file.
> >> >> > For
> >> >> > some time steps, a single box is drawn, for other time steps I can
> >> >> > have
> >> >> > many
> >> >> > of them. Some boxes can disappear and also re-appear at a later
> time
> >> >> > step.
> >> >> >
> >> >> > This means I have "duplicates" boxes. If a box is present at two
> >> >> > different
> >> >> > time steps (with the same "boxname" when calling load_cgo()), it
> will
> >> >> > be
> >> >> > created in pymol multiple times, but the "timestep" option of the
> >> >> > "load_cgo()" command should make it appear at the right time step.
> >> >> >
> >> >> > Unfortunately, it is not working as expected. All the boxes are
> drawn
> >> >> > correctly and they appear at the righ time. BUT, some of them are
> not
> >> >> > "hidden" (or deleted) when they should.
> >> >> >
> >> >> > As an example, I'm attaching a webm video of a particle travelling
> >> >> > from
> >> >> > right to left (white ball). The initial frame is correct: the boxes
> >> >> > are
> >> >> > correctly drawn where I want them. As the particle travels, boxes
> >> >> > should
> >> >> > adapt to its location. New boxes are created fine: as the particle
> is
> >> >> > traveling, we can see boxes adjusting around it. But the two
> smallest
> >> >> > boxes
> >> >> > are always shown while they should not appear starting from half of
> >> >> > the
> >> >> > movie.
> >> >> >
> >> >> > In the loop which creates the CGO objects, I print the box
> properties
> >> >> > to
> >> >> > verify that I don't add the two small boxes when they shouldn't
> >> >> > appear.
> >> >> > Except from that, I don't know what else could be wrong. Maybe I'm
> >> >> > abusing
> >> >> > the "state" argument to load_cgo() or not using it correctly?
> >> >> >
> >> >> > Thank you for any help!
> >> >> >
> >> >> > Nicolas
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> ------------------------------------------------------------------------------
> >> >> > What You Don't Know About Data Connectivity CAN Hurt You
> >> >> > This paper provides an overview of data connectivity, details
> >> >> > its effect on application quality, and explores various alternative
> >> >> > solutions. http://p.sf.net/sfu/progress-d2d
> >> >> > _______________________________________________
> >> >> > PyMOL-users mailing list ([email protected])
> >> >> > Info Page:
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> >> > Archives:
> >> >> > http://www.mail-archive.com/[email protected]
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Jason Vertrees, PhD
> >> >> PyMOL Product Manager
> >> >> Schrodinger, LLC
> >> >>
> >> >> (e) [email protected]
> >> >> (o) +1 (603) 374-7120
> >> >
> >> >
> >> >
> >> >
> ------------------------------------------------------------------------------
> >> > What You Don't Know About Data Connectivity CAN Hurt You
> >> > This paper provides an overview of data connectivity, details
> >> > its effect on application quality, and explores various alternative
> >> > solutions. http://p.sf.net/sfu/progress-d2d
> >> > _______________________________________________
> >> > PyMOL-users mailing list ([email protected])
> >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> > Archives:
> http://www.mail-archive.com/[email protected]
> >> >
> >>
> >>
> >>
> >> --
> >> Jason Vertrees, PhD
> >> PyMOL Product Manager
> >> Schrodinger, LLC
> >>
> >> (e) [email protected]
> >> (o) +1 (603) 374-7120
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> What You Don't Know About Data Connectivity CAN Hurt You
> >> This paper provides an overview of data connectivity, details
> >> its effect on application quality, and explores various alternative
> >> solutions. http://p.sf.net/sfu/progress-d2d
> >> _______________________________________________
> >> PyMOL-users mailing list ([email protected])
> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> Archives: http://www.mail-archive.com/[email protected]
> >
> >
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) [email protected]
> (o) +1 (603) 374-7120
>
------------------------------------------------------------------------------
What You Don't Know About Data Connectivity CAN Hurt You
This paper provides an overview of data connectivity, details
its effect on application quality, and explores various alternative
solutions. http://p.sf.net/sfu/progress-d2d
_______________________________________________
PyMOL-users mailing list ([email protected])
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/[email protected]
