[PyMOL] Finding RNA/DNA complementary base pairs using PyMOL

2017-03-13 Thread Paweł Tomaszewski
Dear all,
Is there a function or script which in simple way can find a complementary
base-pairs in my (deoxy)ribonucleic acid?

Suppose I have some double stranded RNA/DNA structure loaded into PyMOL.
Now I've chosen some nocleotyde or set of many nucleotydes and just want to
find residues of its complementary base-pairs (A-T, A-U, C-G).

Thanks a lot,
Paweł
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Re: [PyMOL] VR for Pymol?

2016-08-16 Thread Paweł Tomaszewski
Hello,
That's not a big deal but I am working on some project where you can
interactively explore protein structure in PyMOL using some VR device in my
case this is SensAble Phantom Omni.

You can watch first working version of my project here (video is in polish,
but you can ask any questions in comments or here on PyMOL mailing list):
https://www.youtube.com/watch?v=JySK4F6PYLs


Thank you
Paweł Tomaszewski


2016-06-17 15:47 GMT+02:00 Albert <mailmd2...@gmail.com>:

> Hello:
>
> Does anybody have any idea whether PyMol support Virtual Reality (VR)?
> Can we use the following VR devices to visualize PyMOl in computer?
>
> http://www.polygon.com/2016/1/5/10719326/nvidia-virtual-
> reality-performance-power
>
> https://www.youtube.com/watch?v=U4JPhUr_d7g
>
> If yes, will any VR device on the market work for PyMol?
>
> Thanks a lot
>
> 
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Re: [PyMOL] How to get TTT matrix in PyMOL 1.7.6?

2015-08-18 Thread Paweł Tomaszewski
Thanks Jared,
I have tried the transformations.py script, and here is what I've got:
- I get a quaternions from external source (a 3d manipulator) in a
classical form: [x,y,z,w]
- I use function: quaternion_matrix(quaternion) from transformations.py
script:

m = quaternion_matrix([x, y, z, w])# m is an array of an arrays (4x4)
M = [m[0,0], m[0,1], m[0,2], m[0,3], m[1,0], m[1,1], m[1,2], m[1,3],
m[2,0], m[2,1], m[2,2], m[2,3], m[3,0], m[3,1], m[3,2], m[3,3]]   # so i
need to convert it to a vector 16x1
cmd.transform_selection(all, M, homogenous=1)  # its time to apply the
vector into a transform_selection function; homogenous=0 also doesn't work
print M # print works fine ;)

But the function transform_selection does not work and I don't really know
why, rotation doesn't occur.
Maybe it's because the selection is wrong? On the scene I have a CGO (an
arrow) and even when I change the selection string from all to arrow it
doesn't rotate either.
What exactly is the selection, could this be a CGO?

I have also noticed, that function cmd.rotate(...) works for my CGO arrow
when I set property object=arrow and I put some arbitrary hardcoded
parameters (axis and angle).
Maybe the better way would be use this function?
But I'm not really sure which function from transformations.py script
should I use to convert quaternions to axis and angle params required by
cmd.rotate() function...
any ideas?

Cheers,
Pawel T.





2015-08-13 18:34 GMT+02:00 Sampson, Jared jared.samp...@nyumc.org:

 Hi Paweł -

 Honestly, if you prefer to use matrices, I'd say just go ahead and use
 get_object_matrix; I doubt it's going away any time soon.  You may want to
 use this in combination with transform_selection
 http://www.pymolwiki.org/index.php/Transform_selection.

 Also maybe check out Christoph Gohlke's transformations.py script
 http://www.pymolwiki.org/index.php/Transformations.  It offers several
 tools for manipulating quaternions, matrices, and angle/axis operations.  I
 think there's also a newer version on his website, which is linked from the
 wiki page.

 Cheers,
 Jared

 --
 Jared Sampson
 Xiangpeng Kong Lab
 NYU Langone Medical Center
 http://kong.med.nyu.edu/






 On Aug 6, 2015, at 4:04 AM, Paweł Tomaszewski croov...@gmail.com wrote:

 Hello,
 I've created a CGO in pymol script (a cone) and I need to make some
 transformations on it. I've found that it is easier for me to modify a TTT
 matrix rather than using translate/rotate functions.

 Documentation says [http://www.pymolwiki.org/index.php/Get_object_matrix]
 get_object_matrix is unsupported operation. So how to get/set TTT?

 The problem is, that I get (from external source) position in quaternions
 and now I need to make my CGO position equal to those quaternion. How can I
 make it work?

 Thanks
 Paweł Tomaszewski

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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.



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Re: [PyMOL] WARNING: glDrawBuffer caused GL error on windows 7

2014-02-18 Thread Paweł Tomaszewski
Hi Camilo.

I've got the same error! But it seems, there's no simple solution for this.
Where do you have your PyMOL from?

Cheers
Pawel


2014-02-18 2:08 GMT+01:00 Camilo Andrés Jimenez Cruz 
camilo.jimen...@gmail.com:

 Hi everybody

 I installed pymol 1.6.x unofficial in windows 7 home. As far as I have
 tested it works well, but the console (as in the screen that the GL window
 shows when I press escape) and the main window keep constantly showing the
 message

  WARNING: glDrawBuffer caused GL error

 which is annoying because I can't see the help or any other output to
 there.

 Any ideas on how to tackle this?

 Thanks

 -- Camilo Jiménez


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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.


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