Re: [PyMOL] Cartoon transparency

2013-06-06 Thread Noinaj, Nicholas (NIH/NIDDK) [F] 
Not sure if u have solved this yet, but see 'cartoon skip', i think that is 
what u r looking for.

Cheers
Nick



From: Gianluigi Caltabiano [chimic...@yahoo.it]
Sent: Thursday, June 06, 2013 7:50 
To: James Starlight; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Cartoon transparency

You need to create a new object of the part you want transparent and then set 
that cartoon as transparent (and hide the "original" cartoon for the selection).

G.


Da: James Starlight 
A: pymol-users 
Inviato: Giovedì 6 Giugno 2013 12:36
Oggetto: [PyMOL] Cartoon transparency

Dear PyMol users!


I want to set transparency on the selected carton region of my protein ( I have 
closed GFP barell with the chromophore inside it so I'd like set transparency 
of some beta-shits to make chromophore easily visible ).


In PyMol I've selected region corresponded to that Beta-sheets and than used

set cartoon_transparency, 0.5, sele


unfortunatelly there were no any changes after this :(

How I could solve it ?



Thanks for help,


James

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Re: [PyMOL] scenes and atom-wise colors

2013-06-06 Thread Robert Hanson 
[responding to Folmer Fredslund, private message]

Thanks, Folmer. What I was missing was the difference between

  color colorName, selection

and

  set xxx_color, colorName

and

  set xxx_color, colorName, selection

Each of which does something totally different internally in PyMOL. I see
now that scenes only reproduce the first of these. That is, they only set
the "inherited" color of atoms that we see specifically when the
representation color (dot_color, ribbon_color, sphere_color, etc, set by
the second and third of these commands) is set to -1.

That's what was throwing me off.

For my purposes, it just means that I have to be careful to use only the
COLOR command if I want scenes to reproduce changes in color.

Might be nice to explain that on the wiki. (Or, of course, maybe  I missed
it there)

Bob




On Thu, Jun 6, 2013 at 9:47 AM, Robert Hanson  wrote:

> I guess I still don't understand exactly what a scene is:
>
> "scene" saves and restores scenes.  A scene consists of the camera
> view, all object activity information, all atom-wise visibilities,
> all atom-wise colors, all representations, the global frame index,
> and may contain a text message to display on playback.
>
> I get all of that except colors. How does that work in terms of "atom-wise
> colors" ?
> When does the scene change colors? That is, what commands would I issue
> that would set colors that would be recalled by a scene change?
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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[PyMOL] scenes and atom-wise colors

2013-06-06 Thread Robert Hanson 
I guess I still don't understand exactly what a scene is:

"scene" saves and restores scenes.  A scene consists of the camera
view, all object activity information, all atom-wise visibilities,
all atom-wise colors, all representations, the global frame index,
and may contain a text message to display on playback.

I get all of that except colors. How does that work in terms of "atom-wise
colors" ?
When does the scene change colors? That is, what commands would I issue
that would set colors that would be recalled by a scene change?



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
How ServiceNow helps IT people transform IT departments:
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Re: [PyMOL] Cartoon transparency

2013-06-06 Thread Robert Hanson 
That would not work if you were trying to show selected individual ribbon
segments translucent, I think. Right?

>From what I can tell, here is the list of settings that you can assign a
selection. Notably missing is cartoon_transparency and ribbon_transparency.
Perhaps because a cartoon object can't be broken down into individual
segments that way in PyMOL.  Are there more?

cartoon_color
dot_color
ellipsoid_color
ellipsoid_scale
ellipsoid_transparency
label_color
label_position
ladder_color
ladder_mode
ladder_radius
mesh_color
nonbonded_transparency
ribbon_color
ring_color
ring_mode
ring_radius
ring_width
sphere_color
sphere_scale
sphere_transparency
surface_color
transparency






On Thu, Jun 6, 2013 at 6:50 AM, Gianluigi Caltabiano wrote:

> You need to create a new object of the part you want transparent and then
> set that cartoon as transparent (and hide the "original" cartoon for the
> selection).
>
> G.
>
>   --
>  *Da:* James Starlight 
> *A:* pymol-users 
> *Inviato:* Giovedì 6 Giugno 2013 12:36
> *Oggetto:* [PyMOL] Cartoon transparency
>
> Dear PyMol users!
>
>
> I want to set transparency on the selected carton region of my protein ( I
> have closed GFP barell with the chromophore inside it so I'd like set
> transparency of some beta-shits to make chromophore easily visible ).
>
>
> In PyMol I've selected region corresponded to that Beta-sheets and than
> used
>
> set cartoon_transparency, 0.5, sele
>
>
>
> unfortunatelly there were no any changes after this :(
>
> How I could solve it ?
>
>
>
> Thanks for help,
>
>
> James
>
>
> --
> How ServiceNow helps IT people transform IT departments:
> 1. A cloud service to automate IT design, transition and operations
> 2. Dashboards that offer high-level views of enterprise services
> 3. A single system of record for all IT processes
> http://p.sf.net/sfu/servicenow-d2d-j
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>
>
>
> --
> How ServiceNow helps IT people transform IT departments:
> 1. A cloud service to automate IT design, transition and operations
> 2. Dashboards that offer high-level views of enterprise services
> 3. A single system of record for all IT processes
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>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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Re: [PyMOL] Cartoon transparency

2013-06-06 Thread Gianluigi Caltabiano 
You need to create a new object of the part you want transparent and then set 
that cartoon as transparent (and hide the "original" cartoon for the 
selection). 

G.



 Da: James Starlight 
A: pymol-users  
Inviato: Giovedì 6 Giugno 2013 12:36
Oggetto: [PyMOL] Cartoon transparency
 


Dear PyMol users!


I want to set transparency on the selected 
carton region of my protein ( I have closed GFP barell with the 
chromophore inside it so I'd like set transparency of some beta-shits to
 make chromophore easily visible ).


In PyMol I've selected region corresponded to that Beta-sheets and than used

set cartoon_transparency, 0.5, sele 

unfortunatelly there were no any changes after this :(

How I could solve it ?



Thanks for help,


James

--
How ServiceNow helps IT people transform IT departments:
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[PyMOL] Cartoon transparency

2013-06-06 Thread James Starlight 
Dear PyMol users!


I want to set transparency on the selected carton region of my protein ( I
have closed GFP barell with the chromophore inside it so I'd like set
transparency of some beta-shits to make chromophore easily visible ).


In PyMol I've selected region corresponded to that Beta-sheets and than used

set cartoon_transparency, 0.5, sele



unfortunatelly there were no any changes after this :(

How I could solve it ?



Thanks for help,


James
--
How ServiceNow helps IT people transform IT departments:
1. A cloud service to automate IT design, transition and operations
2. Dashboards that offer high-level views of enterprise services
3. A single system of record for all IT processes
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