[Chimera-users] Color marker and bonds

[Tom Goddard]

Hi Karine,

  Maybe you mean you were trying to edit the Chimera session (file.py) you attached to your original message.  That will be very hard to edit.   I assume some code generated all the bond colors by computing the angles you mentioned.  It is that code that did the original coloring (before the session was saved) that should be modified to also color the atoms/markers.

	Tom


> On Nov 17, 2020, at 6:09 AM, karine.gouriet <karine.gouriet at univ-lille.fr> wrote:
> 
> Hi Tom,
> 
> thank you for you response. I'm not a specialist of python code, but I modify already the initial code, to change the color of the markers and bonds, but nothing appears for the markers. Maybe I forget something, because all the markers (which I suppose are the atoms) have the same color, wrote in the general routine for one marker. Do you where should I insert the command to change that ?
> 
> thank you a lot for your help. Chimera is a nice software to dislocation tomography.
> 
> best regards
> 
> Karine
> 
> Le 16/11/2020 à 19:23, Tom Goddard a écrit :
>> Hi Karine,
>> 
>>   There is no Chimera setting that sets atom color to match bond color.  The path in your attached session, each atom has two bonds, so I guess you would want it to have the average color of the bonds.  What code or commands colored the bonds?  If some custom code colored the bonds it could also easily color the atoms with a few more lines of code.
>> 
>>   Some Python code that you could open in Chimera could recolor the atoms to the average of the connected bonds it you have no way to edit the code that produced the original coloring to make it color the atoms.
>> 
>> 	Tom
>> 
>> 
>>> On Nov 16, 2020, at 1:44 AM, karine.gouriet <karine.gouriet at univ-lille.fr> wrote:
>>> 
>>> Dear all
>>> 
>>> we want to correspond the marker color with the bond color. here the bond color is the angle of the scalar product of the bond line and another vector.
>>> 
>>> It is possible to change the marker color by the bond color and not the inverse ?
>>> 
>>> Thanks a lot for your help.
>>> 
>>> PS: I joint the file.py corresponding to the modification of rgba function we want.
>>> 
>>> -- 
>>> --------------------------------------
>>> Karine GOURIET
>>> Maître de Conférences
>>> tel : 03.20.43.43.98.
>>> Unité Matériaux et Transformation
>>> CNRS UMR 8207 - Université de Lille 1
>>> Bat C6, Bureau 213
>>> 59655 Villeneuve D'ascq
>>> http://umet.univ-lille1.fr/
>>> --------------------------------------
>>> 
>>> <file.py>_______________________________________________
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> 
> -- 
> --------------------------------------
> Karine GOURIET
> Maître de Conférences
> tel : 03.20.43.43.98.
> Unité Matériaux et Transformation
> CNRS UMR 8207 - Université de Lille 1
> Bat C6, Bureau 213
> 59655 Villeneuve D'ascq
> http://umet.univ-lille1.fr/
> --------------------------------------
> 
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