Re: [PyMOL] feature request

2019-10-01 Thread Oganesyan, Vaheh 
Thomas and Jared,
I’m not sure what will be the best solution, but as a start, color of the 
object name may stay white if more than one color is used. Because you both 
found this as an interesting idea allows me to ask similar question now 
regarding labels. What if we can get label_color match the residue color. I 
vaguely remember something like this discussed x number of years ago, but do 
not remember why not. Could label become property of the object and not just a 
property of a session?

Thank you.


From: Jared Sampson 
Sent: Tuesday, October 1, 2019 2:45 PM
To: Oganesyan, Vaheh ; Thomas Holder 

Cc: pymol-users 
Subject: Re: [PyMOL] feature request

Hi Thomas and Vaheh -

This is indeed an interesting idea.  I was thinking about this in terms of 
implementation, and what the edge cases might be.  I wonder what would be the 
mechanism for assigning the color if the object is not just a single color.  
Would it be the color that is the dominant color of the object over all 
(visible) representations?

What about a spectrum-colored object?  Would it be possible to color the object 
name according to the colors in the spectrum (like the "spectrum" and "rainbow" 
menu items already in the OpenGL menu)?

And what if there are different coloring schemes for the different 
representations—would there be a hierarchy in terms of choosing , e.g. surface 
> cartoon > stick > line, etc.?

I definitely like Thomas' idea of a global `internal_gui_name_color_mode` 
setting to turn the menu object name coloring on/off.  (Perhaps different modes 
could correspond to different ways of choosing the displayed color.)  It might 
also be useful to include object-level (or named-selection-level) settings to 
override the global setting and specify the color or spectrum directly, e.g.:

set internal_gui_name_color, red, obj1
set internal_gui_name_spectrum, rainbow, obj1

Really interesting suggestion, Vaheh.  Looking forward to seeing how it might 
work!

Cheers,
Jared


On October 1, 2019 at 5:13:07 AM, Thomas Holder 
(thomas.hol...@schrodinger.com) wrote:
Hi Vaheh,

I see that this can be useful, and it's fairly easy to implement. We can add a 
new setting to turn this on and off, like "internal_gui_name_color_mode" (or do 
you have a suggestion for a better name?).

Cheers,
Thomas


> On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh 
> mailto:vaheh.oganes...@astrazeneca.com>> 
> wrote:
>
> Thomas and other PyMOL developers,
>
> It looks as if we color the object name similar to the object color it will 
> be easier to distinguish which structure am I manipulating now. While models 
> can be colored, the names of the models can't.
> Anybody else think it might be helpful?
>
> Thank you.
> Regards,
>
> Vaheh Oganesyan, Ph.D.
> Scientist, Biologic Therapeutics
> 
> AstraZeneca
> R | Antibody Discovery and Protein Engineering
> One Medimmune Way, Gaithersburg, MD 20878
> T: 301-398-4640 M: 240-398-0046
> vaheh.oganes...@astrazeneca.com

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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Re: [PyMOL] feature request

2019-10-01 Thread Jared Sampson 
Hi Thomas and Vaheh - 

This is indeed an interesting idea.  I was thinking about this in terms of 
implementation, and what the edge cases might be.  I wonder what would be the 
mechanism for assigning the color if the object is not just a single color.  
Would it be the color that is the dominant color of the object over all 
(visible) representations?

What about a spectrum-colored object?  Would it be possible to color the object 
name according to the colors in the spectrum (like the "spectrum" and "rainbow" 
menu items already in the OpenGL menu)?

And what if there are different coloring schemes for the different 
representations—would there be a hierarchy in terms of choosing , e.g. surface 
> cartoon > stick > line, etc.?

I definitely like Thomas' idea of a global `internal_gui_name_color_mode` 
setting to turn the menu object name coloring on/off.  (Perhaps different modes 
could correspond to different ways of choosing the displayed color.)  It might 
also be useful to include object-level (or named-selection-level) settings to 
override the global setting and specify the color or spectrum directly, e.g.:

    set internal_gui_name_color, red, obj1
    set internal_gui_name_spectrum, rainbow, obj1

Really interesting suggestion, Vaheh.  Looking forward to seeing how it might 
work!

Cheers,
Jared

On October 1, 2019 at 5:13:07 AM, Thomas Holder (thomas.hol...@schrodinger.com) 
wrote:

Hi Vaheh,

I see that this can be useful, and it's fairly easy to implement. We can add a 
new setting to turn this on and off, like "internal_gui_name_color_mode" (or do 
you have a suggestion for a better name?).

Cheers,
Thomas


> On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh 
>  wrote:
>  
> Thomas and other PyMOL developers,
>  
> It looks as if we color the object name similar to the object color it will 
> be easier to distinguish which structure am I manipulating now. While models 
> can be colored, the names of the models can't.
> Anybody else think it might be helpful?
>  
> Thank you.
> Regards,
>  
> Vaheh Oganesyan, Ph.D.
> Scientist, Biologic Therapeutics
> 
> AstraZeneca
> R | Antibody Discovery and Protein Engineering
> One Medimmune Way, Gaithersburg, MD 20878
> T: 301-398-4640 M: 240-398-0046  
> vaheh.oganes...@astrazeneca.com

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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Re: [PyMOL] feature request

2019-10-01 Thread Thomas Holder 
Hi Vaheh,

I see that this can be useful, and it's fairly easy to implement. We can add a 
new setting to turn this on and off, like "internal_gui_name_color_mode" (or do 
you have a suggestion for a better name?).

Cheers,
  Thomas


> On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh 
>  wrote:
> 
> Thomas and other PyMOL developers,
> 
> It looks as if we color the object name similar to the object color it will 
> be easier to distinguish which structure am I manipulating now. While models 
> can be colored, the names of the models can't.
> Anybody else think it might be helpful?
> 
> Thank you.
> Regards,
> 
> Vaheh Oganesyan, Ph.D.
> Scientist, Biologic Therapeutics
> 
> AstraZeneca
> R | Antibody Discovery and Protein Engineering
> One Medimmune Way, Gaithersburg, MD 20878
> T:  301-398-4640  M:  240-398-0046 
> vaheh.oganes...@astrazeneca.com

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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