Re: [PyMOL] Yaw, Pitch and Roll of CGO

2014-02-18 Thread Thomas Holder
Hi Pawel,

you should read

PyMOL help(cmd.rotate)

This would tell you that the rotate function has a origin argument.

Hope that helps.

Cheers,
  Thomas

On 17 Feb 2014, at 14:40, Paweł Tomaszewski croov...@gmail.com wrote:

 Thank you Thomas
 Using camera=0 caused my cone not to do rotations related to the camera 
 position. 
 Cone still rotates not about itself, but about axis of global coordinate 
 system.
 Do you have any other ideas?
 
 Cheers, 
Paweł
 
 
 2014-02-06 17:00 GMT+01:00 Thomas Holder thomas.hol...@schrodinger.com:
 Hi Pawel,
 
 have you tried using the camera=0 argument?
 
 cmd.rotate(axis, angle, object='yourcone', camera=0)
 
 Cheers,
   Thomas
  
 On 05 Feb 2014, at 15:46, Павел Томашевский croov...@gmail.com wrote:
 
  Hello
  I've made a cone CGO (something like a pointer) and now I need to make a 
  rotation of the cone. I have got yaw, pitch and roll angle values, but when 
  I do 'rotate' command it rotates about axis of the global coordinate system.
 
  My question is, how to make a rotation of the CGO about axis that is NOT of 
  the global pymol coordinate system but goes through the CGO itself?
 
  I hope it's clear what I mean ;)
 
  Thank you
  Pawel

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.


--
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Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
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Re: [PyMOL] Yaw, Pitch and Roll of CGO

2014-02-18 Thread Sampson, Jared
Hi Pawel -

If you can determine the primary axis of the cone from the tip and the center 
of the circle at the base, you can give `rotate` an arbitrary [x,y,z] float 
vector as its first argument instead of x, y or z.  For example, if you 
generate your cone using something like the following Python script:

### cone_cgo.py ###

from pymol.cgo import *
from pymol import cmd

# set up the cone
base_xyz = [1.0, 2.0, 3.0]
tip_xyz = [4.0, 5.0, 6.0]
base_radius = 1.0
tip_radius = 0.0
base_color = [0.9, 0.0, 0.0]
tip_color = [0.0, 0.0, 0.9]

# calculate the cone axis
cone_axis = [ tip_xyz[0]-base_xyz[0],
  tip_xyz[1]-base_xyz[1],
  tip_xyz[2]-base_xyz[2] ]

# print the axis to use later
print cone_axis

# generate the cone CGO text
obj = [CONE, base_xyz[0], base_xyz[1], base_xyz[2], tip_xyz[0], tip_xyz[1], 
tip_xyz[2], base_radius, tip_radius, base_color[0], base_color[1], 
base_color[2], tip_color[0], tip_color[1], tip_color[2], 1, 1]

# load it
cmd.load_cgo(obj, 'cone')

# generate a pseudoatom for reference
cmd.pseudoatom('point', pos=[2,5,4])
cmd.show_as('nb_spheres', 'point')

### end cone_cgo.py ###

and load it via `run cone_cgo.py`, then you can rotate the cone on its axis 
using, e.g.:

rotate [3,3,3], 10, object=cone, camera=0

Even with a radially symmetric cone surface, if you look closely, you can see 
the individual polygons changing at the cone base.  You can also rotate the 
scene around the cone axis with, e.g.:

rotate [3,3,3], 10

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/






On Feb 17, 2014, at 2:40 PM, Paweł Tomaszewski 
croov...@gmail.commailto:croov...@gmail.com wrote:

Thank you Thomas
Using camera=0 caused my cone not to do rotations related to the camera 
position.
Cone still rotates not about itself, but about axis of global coordinate system.
Do you have any other ideas?

Cheers,
   Paweł


2014-02-06 17:00 GMT+01:00 Thomas Holder 
thomas.hol...@schrodinger.commailto:thomas.hol...@schrodinger.com:
Hi Pawel,

have you tried using the camera=0 argument?

cmd.rotate(axis, angle, object='yourcone', camera=0)

Cheers,
  Thomas

On 05 Feb 2014, at 15:46, Павел Томашевский 
croov...@gmail.commailto:croov...@gmail.com wrote:

 Hello
 I've made a cone CGO (something like a pointer) and now I need to make a 
 rotation of the cone. I have got yaw, pitch and roll angle values, but when I 
 do 'rotate' command it rotates about axis of the global coordinate system.

 My question is, how to make a rotation of the CGO about axis that is NOT of 
 the global pymol coordinate system but goes through the CGO itself?

 I hope it's clear what I mean ;)

 Thank you
 Pawel


--
Thomas Holder
PyMOL Developer
Schrödinger, Inc.


--
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
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Re: [PyMOL] Yaw, Pitch and Roll of CGO

2014-02-18 Thread Paweł Tomaszewski
Jared, Thomas thank you guys!

Now everything works great :)
The solution was pretty simple and I don't know why it took me so long...
I have a X,Y and Z coordinates from my SensAble Pantom haptic device and
quaternions to do rotations of cone.

The problem was, that in 'translate' function I didn't use 'camera=0'
option, what in did in 'rotate'. Moreover I should set 'origin=[X,Y,Z]'
option as well as 'camera=0' in rotate option.

Now it work smoothly and pretty nice ;)

Thank you
Paweł



2014-02-18 19:40 GMT+01:00 Sampson, Jared jared.samp...@nyumc.org:

  Hi Pawel -

  If you can determine the primary axis of the cone from the tip and the
 center of the circle at the base, you can give `rotate` an arbitrary
 [x,y,z] float vector as its first argument instead of x, y or z.  For
 example, if you generate your cone using something like the following
 Python script:

  ### cone_cgo.py ###

   from pymol.cgo import *
 from pymol import cmd

  # set up the cone
 base_xyz = [1.0, 2.0, 3.0]
 tip_xyz = [4.0, 5.0, 6.0]
 base_radius = 1.0
 tip_radius = 0.0
 base_color = [0.9, 0.0, 0.0]
 tip_color = [0.0, 0.0, 0.9]

  # calculate the cone axis
 cone_axis = [ tip_xyz[0]-base_xyz[0],
   tip_xyz[1]-base_xyz[1],
   tip_xyz[2]-base_xyz[2] ]

  # print the axis to use later
 print cone_axis

  # generate the cone CGO text
 obj = [CONE, base_xyz[0], base_xyz[1], base_xyz[2], tip_xyz[0],
 tip_xyz[1], tip_xyz[2], base_radius, tip_radius, base_color[0],
 base_color[1], base_color[2], tip_color[0], tip_color[1], tip_color[2], 1,
 1]

  # load it
 cmd.load_cgo(obj, 'cone')

  # generate a pseudoatom for reference
 cmd.pseudoatom('point', pos=[2,5,4])
 cmd.show_as('nb_spheres', 'point')

   ### end cone_cgo.py ###


  and load it via `run cone_cgo.py`, then you can rotate the cone on its
 axis using, e.g.:

  rotate [3,3,3], 10, object=cone, camera=0


  Even with a radially symmetric cone surface, if you look closely, you
 can see the individual polygons changing at the cone base.  You can also
 rotate the scene around the cone axis with, e.g.:

   rotate [3,3,3], 10


  Hope that helps.

  Cheers,
 Jared

 --
 Jared Sampson
 Xiangpeng Kong Lab
 NYU Langone Medical Center
 550 First Avenue
 New York, NY 10016
 212-263-7898
 http://kong.med.nyu.edu/






  On Feb 17, 2014, at 2:40 PM, Paweł Tomaszewski croov...@gmail.com
 wrote:

  Thank you Thomas
 Using camera=0 caused my cone not to do rotations related to the camera
 position.
 Cone still rotates not about itself, but about axis of global coordinate
 system.
 Do you have any other ideas?

  Cheers,
Paweł


 2014-02-06 17:00 GMT+01:00 Thomas Holder thomas.hol...@schrodinger.com:

 Hi Pawel,

 have you tried using the camera=0 argument?

 cmd.rotate(axis, angle, object='yourcone', camera=0)

 Cheers,
   Thomas


  On 05 Feb 2014, at 15:46, Павел Томашевский croov...@gmail.com wrote:

  Hello
  I've made a cone CGO (something like a pointer) and now I need to make
 a rotation of the cone. I have got yaw, pitch and roll angle values, but
 when I do 'rotate' command it rotates about axis of the global coordinate
 system.
 
  My question is, how to make a rotation of the CGO about axis that is
 NOT of the global pymol coordinate system but goes through the CGO itself?
 
  I hope it's clear what I mean ;)
 
  Thank you
  Pawel


  --
 Thomas Holder
 PyMOL Developer
 Schrödinger, Inc.



 --
 Managing the Performance of Cloud-Based Applications
 Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
 Read the Whitepaper.

 http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net


  
 This email message, including any attachments, is for the sole use of the
 intended recipient(s) and may contain information that is proprietary,
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 unauthorized review, use, disclosure, or distribution is prohibited. If you
 have received this email in error please notify the sender by return email
 and delete the original message. Please note, the recipient should check
 this email and any attachments for the presence of viruses. The
 organization accepts no liability for any damage caused by any virus
 transmitted by this email.
 =

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Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.

Re: [PyMOL] Yaw, Pitch and Roll of CGO

2014-02-18 Thread Sampson, Jared
Hi Pawel -

Glad you were able to make it work.  Also, that haptic device (I guess the new 
version is the Geomagic Touch?) looks pretty neat.

I'm now realizing that when you asked how to make a rotation of the CGO about 
axis that is NOT of the global pymol coordinate system but goes through the CGO 
itself you probably didn't necessarily mean a rotation about the cone's 
primary axis, because that doesn't really do a whole lot unless your object 
isn't radially symmetric!

For correctness' sake, however, I need to amend my previous response.  It turns 
out I chose unfortunate values for the cone base and tip positions in my 
example, which resulted in the cone axis going through the global coordinate 
origin.  My previous attempt fails for cones that don't point at or away from 
the origin.  Whoops!

Thomas'  suggestion about the origin argument fixes it, though.  So for my 
example, I'd also need either the tip or the base position:

# print the values to use later
print tip_xyz = %s % tip_xyz   # need this, too!
print axis = %s % cone_axis

and then rotate the cone with, e.g.:

rotate [3,3,3], 10, object=cone, camera=0, origin=[4,5,6]

or everything with, e.g.:

rotate [3,3,3], 10, origin=[4,5,6]

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/






On Feb 18, 2014, at 2:04 PM, Paweł Tomaszewski 
croov...@gmail.commailto:croov...@gmail.com
 wrote:

Jared, Thomas thank you guys!

Now everything works great :)
The solution was pretty simple and I don't know why it took me so long...
I have a X,Y and Z coordinates from my SensAble Pantom haptic device and 
quaternions to do rotations of cone.

The problem was, that in 'translate' function I didn't use 'camera=0' option, 
what in did in 'rotate'. Moreover I should set 'origin=[X,Y,Z]' option as well 
as 'camera=0' in rotate option.

Now it work smoothly and pretty nice ;)

Thank you
Paweł



2014-02-18 19:40 GMT+01:00 Sampson, Jared 
jared.samp...@nyumc.orgmailto:jared.samp...@nyumc.org:
Hi Pawel -

If you can determine the primary axis of the cone from the tip and the center 
of the circle at the base, you can give `rotate` an arbitrary [x,y,z] float 
vector as its first argument instead of x, y or z.  For example, if you 
generate your cone using something like the following Python script:

### cone_cgo.py ###

from pymol.cgo import *
from pymol import cmd

# set up the cone
base_xyz = [1.0, 2.0, 3.0]
tip_xyz = [4.0, 5.0, 6.0]
base_radius = 1.0
tip_radius = 0.0
base_color = [0.9, 0.0, 0.0]
tip_color = [0.0, 0.0, 0.9]

# calculate the cone axis
cone_axis = [ tip_xyz[0]-base_xyz[0],
  tip_xyz[1]-base_xyz[1],
  tip_xyz[2]-base_xyz[2] ]

# print the axis to use later
print cone_axis

# generate the cone CGO text
obj = [CONE, base_xyz[0], base_xyz[1], base_xyz[2], tip_xyz[0], tip_xyz[1], 
tip_xyz[2], base_radius, tip_radius, base_color[0], base_color[1], 
base_color[2], tip_color[0], tip_color[1], tip_color[2], 1, 1]

# load it
cmd.load_cgo(obj, 'cone')

# generate a pseudoatom for reference
cmd.pseudoatom('point', pos=[2,5,4])
cmd.show_as('nb_spheres', 'point')

### end cone_cgo.py ###

and load it via `run cone_cgo.py`, then you can rotate the cone on its axis 
using, e.g.:

rotate [3,3,3], 10, object=cone, camera=0

Even with a radially symmetric cone surface, if you look closely, you can see 
the individual polygons changing at the cone base.  You can also rotate the 
scene around the cone axis with, e.g.:

rotate [3,3,3], 10

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/






On Feb 17, 2014, at 2:40 PM, Paweł Tomaszewski 
croov...@gmail.commailto:croov...@gmail.com wrote:

Thank you Thomas
Using camera=0 caused my cone not to do rotations related to the camera 
position.
Cone still rotates not about itself, but about axis of global coordinate system.
Do you have any other ideas?

Cheers,
   Paweł


2014-02-06 17:00 GMT+01:00 Thomas Holder 
thomas.hol...@schrodinger.commailto:thomas.hol...@schrodinger.com:
Hi Pawel,

have you tried using the camera=0 argument?

cmd.rotate(axis, angle, object='yourcone', camera=0)

Cheers,
  Thomas

On 05 Feb 2014, at 15:46, Павел Томашевский 
croov...@gmail.commailto:croov...@gmail.com wrote:

 Hello
 I've made a cone CGO (something like a pointer) and now I need to make a 
 rotation of the cone. I have got yaw, pitch and roll angle values, but when I 
 do 'rotate' command it rotates about axis of the global coordinate system.

 My question is, how to make a rotation of the CGO about axis that is NOT of 
 the global pymol coordinate system but goes through the CGO itself?

 I hope it's clear what I mean ;)

 Thank you
 Pawel


--
Thomas Holder
PyMOL Developer
Schrödinger, Inc.


--
Managing the 

Re: [PyMOL] Yaw, Pitch and Roll of CGO

2014-02-18 Thread Paweł Tomaszewski
Jared, my haptic device is SensAble Phantom Omni and now it is called
Geomagic Touch. I work on integration it with PyMOL and VRPN.

So far so good, but now I have a little more complicated problem with
rotate and translate functions.

When I set camera=0 in both of them, it doesn't matter if I move the screen
with mouse or not - my cone rotations and translations are absolute to the
global origin.
But when I don't set camera=0 option translations of the cone still works
well but rotations don't.

I think this is because translate function gets coordinates that are not
absolute to the origin but it gets changes - I mean [dx, dy, dz], where
dx=|x-x0|, x is current position and x0 is previous position (the same with
dy and dz). On the other hand rotate function gets origin option params as
absolute values, here [x, y, z] are cone position. Now after turning camera
with mouse translations of the cone are relative to camera position but
origin of rotation is absolute to main coordinate system position.

In this situation I have two origins: origin of rotations that is equal to
position of the cone and some global PyMOL origin where everything begins.

I hope it's clear so far ;)

Now, is it possible to change the origin of rotation not with values that
are absolute to the global origin but with changes relative to it's
previous position. Or maybe I should ask: Is it possible to CHANGE origin
of rotation, not to SET it?.

I know it's a little complicated to explain what I mean using words, but I
hope I succeeded here ;)

Cheers,
Paweł




2014-02-18 20:24 GMT+01:00 Sampson, Jared jared.samp...@nyumc.org:

  Hi Pawel -

  Glad you were able to make it work.  Also, that haptic device (I guess
 the new version is the Geomagic Touch?) looks pretty neat.

  I'm now realizing that when you asked how to make a rotation of the CGO
 about axis that is NOT of the global pymol coordinate system but goes
 through the CGO itself you probably didn't necessarily mean a rotation
 about the cone's primary axis, because that doesn't really do a whole lot
 unless your object isn't radially symmetric!

  For correctness' sake, however, I need to amend my previous response.
  It turns out I chose unfortunate values for the cone base and tip
 positions in my example, which resulted in the cone axis going through the
 global coordinate origin.  My previous attempt fails for cones that don't
 point at or away from the origin.  Whoops!

  Thomas'  suggestion about the origin argument fixes it, though.  So for
 my example, I'd also need either the tip or the base position:

  # print the values to use later
 print tip_xyz = %s % tip_xyz   # need this, too!
 print axis = %s % cone_axis


  and then rotate the cone with, e.g.:

  rotate [3,3,3], 10, object=cone, camera=0, origin=[4,5,6]


  or everything with, e.g.:

   rotate [3,3,3], 10, origin=[4,5,6]


  Cheers,
 Jared

  --
 Jared Sampson
 Xiangpeng Kong Lab
 NYU Langone Medical Center
 550 First Avenue
 New York, NY 10016
 212-263-7898
 http://kong.med.nyu.edu/






  On Feb 18, 2014, at 2:04 PM, Paweł Tomaszewski croov...@gmail.com
  wrote:

  Jared, Thomas thank you guys!

 Now everything works great :)
 The solution was pretty simple and I don't know why it took me so long...
 I have a X,Y and Z coordinates from my SensAble Pantom haptic device and
 quaternions to do rotations of cone.

  The problem was, that in 'translate' function I didn't use 'camera=0'
 option, what in did in 'rotate'. Moreover I should set 'origin=[X,Y,Z]'
 option as well as 'camera=0' in rotate option.

  Now it work smoothly and pretty nice ;)

  Thank you
 Paweł



 2014-02-18 19:40 GMT+01:00 Sampson, Jared jared.samp...@nyumc.org:

 Hi Pawel -

  If you can determine the primary axis of the cone from the tip and the
 center of the circle at the base, you can give `rotate` an arbitrary
 [x,y,z] float vector as its first argument instead of x, y or z.  For
 example, if you generate your cone using something like the following
 Python script:

  ### cone_cgo.py ###

   from pymol.cgo import *
 from pymol import cmd

  # set up the cone
 base_xyz = [1.0, 2.0, 3.0]
 tip_xyz = [4.0, 5.0, 6.0]
 base_radius = 1.0
 tip_radius = 0.0
 base_color = [0.9, 0.0, 0.0]
 tip_color = [0.0, 0.0, 0.9]

  # calculate the cone axis
 cone_axis = [ tip_xyz[0]-base_xyz[0],
   tip_xyz[1]-base_xyz[1],
   tip_xyz[2]-base_xyz[2] ]

  # print the axis to use later
 print cone_axis

  # generate the cone CGO text
 obj = [CONE, base_xyz[0], base_xyz[1], base_xyz[2], tip_xyz[0],
 tip_xyz[1], tip_xyz[2], base_radius, tip_radius, base_color[0],
 base_color[1], base_color[2], tip_color[0], tip_color[1], tip_color[2], 1,
 1]

  # load it
 cmd.load_cgo(obj, 'cone')

  # generate a pseudoatom for reference
 cmd.pseudoatom('point', pos=[2,5,4])
 cmd.show_as('nb_spheres', 'point')

   ### end cone_cgo.py ###


  and load it via `run cone_cgo.py`, then you can rotate the cone on its
 axis using, e.g.:

  rotate [3,3,3], 

Re: [PyMOL] Yaw, Pitch and Roll of CGO

2014-02-17 Thread Paweł Tomaszewski
Thank you Thomas
Using camera=0 caused my cone not to do rotations related to the camera
position.
Cone still rotates not about itself, but about axis of global coordinate
system.
Do you have any other ideas?

Cheers,
   Paweł


2014-02-06 17:00 GMT+01:00 Thomas Holder thomas.hol...@schrodinger.com:

 Hi Pawel,

 have you tried using the camera=0 argument?

 cmd.rotate(axis, angle, object='yourcone', camera=0)

 Cheers,
   Thomas


 On 05 Feb 2014, at 15:46, Павел Томашевский croov...@gmail.com wrote:

  Hello
  I've made a cone CGO (something like a pointer) and now I need to make a
 rotation of the cone. I have got yaw, pitch and roll angle values, but when
 I do 'rotate' command it rotates about axis of the global coordinate system.
 
  My question is, how to make a rotation of the CGO about axis that is NOT
 of the global pymol coordinate system but goes through the CGO itself?
 
  I hope it's clear what I mean ;)
 
  Thank you
  Pawel


 --
 Thomas Holder
 PyMOL Developer
 Schrödinger, Inc.


--
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Yaw, Pitch and Roll of CGO

2014-02-06 Thread Thomas Holder
Hi Pawel,

have you tried using the camera=0 argument?

cmd.rotate(axis, angle, object='yourcone', camera=0)

Cheers,
  Thomas

On 05 Feb 2014, at 15:46, Павел Томашевский croov...@gmail.com wrote:

 Hello
 I've made a cone CGO (something like a pointer) and now I need to make a 
 rotation of the cone. I have got yaw, pitch and roll angle values, but when I 
 do 'rotate' command it rotates about axis of the global coordinate system.
  
 My question is, how to make a rotation of the CGO about axis that is NOT of 
 the global pymol coordinate system but goes through the CGO itself? 
 
 I hope it's clear what I mean ;)
 
 Thank you
 Pawel


-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.


--
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/4140/ostg.clktrk
___
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[PyMOL] Yaw, Pitch and Roll of CGO

2014-02-05 Thread Павел Томашевский
Hello
I've made a cone CGO (something like a pointer) and now I need to make a
rotation of the cone. I have got yaw, pitch and roll angle values, but when
I do 'rotate' command it rotates about axis of the global coordinate system.

My question is, how to make a rotation of the CGO about axis that is NOT of
the global pymol coordinate system but goes through the CGO itself?

I hope it's clear what I mean ;)

Thank you
Pawel
--
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
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