Re: [PyMOL] on axis of the subunit

[Sampson, Jared M.]

Hi Smith -

I’m not quite sure what you mean by "axis of a subunit."  If you mean the 
principal axis of that selection of atoms, `orient my_selection` will get it 
aligned along one of the axes.  Then you can create pseudoatoms on that axis 
and create a dash between them with the distance command.

# Get it lined up with the viewport axes.
select domain, chain A and resi 1-100
orient domain

# Here I’m assuming this put the long axis of the domain along the
# x axis.  We move the view along the x axis, and place pseudoatoms
# at the viewport center in two places.  You can change the length of the
# displayed axis based on how far you move.
move x, -10
pseudoatom ps1
move x, 20
pseudoatom ps2
move x, -10
distance axis, ps1, ps2

This is a bit clumsy and not a rigorous approach, but it will work for any 
other kind of vector you want to show, as long as you can get it aligned with 
one of the view axes.

Cheers,
Jared

—
Jared Sampson
Graduate Student
Department of Biochemistry and Molecular Biophysics
Columbia University

On Nov 29, 2015, at 7:42 AM, Smith Liu 
> wrote:

Dear All,

Will you please show me how to display an axis of a subunit or a domain by 
pymol?

Smith



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[PyMOL] light reposition

[Дарья Николаева]

Hello,


I want to change the position of my light sources.


First I set the number of light sources:

>set light_count, 3


Then I attempt to reposition the light source, e.g., #2:

>set light2, [x, y, z]


The problem is - I see no changes to the scene.


The question: How to use the "set light(2-8)" command or is there any

other way to reposition light sources?


Thank you,

Darya
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Re: [PyMOL] light reposition

[Schubert, Carsten [JRDUS]]

Darya,

I have never used that feature, but do you see a difference when raytracing or 
drawing the scene? Could be that the regular display mode does not take these 
feature into account (this is a wild guess though)

Cheers,

Carsten

From: Дарья Николаева [mailto:daranikola...@gmail.com]
Sent: Monday, November 30, 2015 9:58 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] light reposition


Hello,



I want to change the position of my light sources.



First I set the number of light sources:

>set light_count, 3



Then I attempt to reposition the light source, e.g., #2:

>set light2, [x, y, z]



The problem is - I see no changes to the scene.



The question: How to use the "set light(2-8)" command or is there any

other way to reposition light sources?



Thank you,

Darya
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Re: [PyMOL] light reposition

[Thomas Holder]

Hi Darya and Carsten,

The "regular display mode" (real-time OpenGL graphics) does take lights into 
account, and their position can be updated in real-time. A neat way to play 
around with lights is in lights mouse mode (new in PyMOL 1.5).

From the menu, select "Mouse > 3 Button Lights"

Now hold down the SHIFT key on the keyboard, press the left mouse button and 
drag (just like rotating the molecule, but now it rotates the light position). 
The "edit_light" setting controls which light get updated.

The effect is most obvious with spheres representation.

Note that "light_count=2" corresponds to one specular light, the first light is 
ambient only.

Cheers,
  Thomas

On 30 Nov 2015, at 13:56, Schubert, Carsten [JRDUS]  
wrote:

> Darya,
>  
> I have never used that feature, but do you see a difference when raytracing 
> or drawing the scene? Could be that the regular display mode does not take 
> these feature into account (this is a wild guess though)
>  
> Cheers,
>  
> Carsten
>  
> From: Дарья Николаева [mailto:daranikola...@gmail.com] 
> Sent: Monday, November 30, 2015 9:58 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] light reposition
>  
> Hello,
>  
> I want to change the position of my light sources.
>  
> First I set the number of light sources:
> >set light_count, 3
>  
> Then I attempt to reposition the light source, e.g., #2:
> >set light2, [x, y, z]
>  
> The problem is - I see no changes to the scene.
>  
> The question: How to use the "set light(2-8)" command or is there any
> other way to reposition light sources?
>  
> Thank you,
> Darya

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] on axis of the subunit

[Sampson, Jared M.]

Hi Smith -

Check out how I did it in the http://pymolwiki.org/index.php/Elbow_angle 
script.  As long as you have the vectors, the angle is easy.  In particular, 
have a look at this line:

elbow = int(numpy.degrees(numpy.arccos(numpy.dot(direction_v, 
direction_c


i.e. the angle (in radians) will be given by the arccos of the dot product of 
the two vectors.  For the elbow angle script, I converted to degrees and 
reported an integer value.

Cheers,
Jared

—
Jared Sampson
Graduate Student
Department of Biochemistry and Molecular Biophysics
Columbia University

On Nov 30, 2015, at 8:33 PM, Smith Liu 
> wrote:


Thanks Jared, it works.

In addition, if by your way I created 2 vectors for 2 different chains, will 
you please show me how to determine the angle formed by the 2 vectors created?

Smith






At 2015-12-01 00:51:46, "Sampson, Jared M." 
> wrote:
Hi Smith -

I’m not quite sure what you mean by "axis of a subunit."  If you mean the 
principal axis of that selection of atoms, `orient my_selection` will get it 
aligned along one of the axes.  Then you can create pseudoatoms on that axis 
and create a dash between them with the distance command.

# Get it lined up with the viewport axes.
select domain, chain A and resi 1-100
orient domain

# Here I’m assuming this put the long axis of the domain along the
# x axis.  We move the view along the x axis, and place pseudoatoms
# at the viewport center in two places.  You can change the length of the
# displayed axis based on how far you move.
move x, -10
pseudoatom ps1
move x, 20
pseudoatom ps2
move x, -10
distance axis, ps1, ps2

This is a bit clumsy and not a rigorous approach, but it will work for any 
other kind of vector you want to show, as long as you can get it aligned with 
one of the view axes.

Cheers,
Jared

—
Jared Sampson
Graduate Student
Department of Biochemistry and Molecular Biophysics
Columbia University

On Nov 29, 2015, at 7:42 AM, Smith Liu 
> wrote:

Dear All,

Will you please show me how to display an axis of a subunit or a domain by 
pymol?

Smith



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Re: [PyMOL] save_transformed.py

[Thomas Holder]

Smith,

Let's take this off-list. I will reply to you directly. We can send a summary 
to the list once it's working for you.

Cheers,
  Thomas

On 29 Nov 2015, at 22:13, Smith Liu  wrote:

> Dear Thomas,
> 
> I do not know I still do something wrong.
> 
> First I load a PDB in pymol, then I input orient (with orient input the 
> molecule really moved significantly in display), then I input 
> transform_by_camera_rotation, then I input save /tmp/withneworientation.pdb, 
> the withneworientation.pdb was really saved, but the newly saved 
> withneworientation.pdb has the all atom orientations (x,y,z) exactly same as 
> those of the original PDB I initially input to the pymol for the process I 
> obtained the withneworientation.pdb.
> 
> Smith

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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