[Chimera-users] [chimera-users]about "color key"

Elaine Meng meng at cgl.ucsf.edu
Wed Dec 22 08:52:46 PST 2010

Hi CJ,
One more idea:  maybe you want Scale Bar (under "Tools... Higher-Order Structure" in the menu) instead of Color Key.


Scale Bar is just a stick with measured length, without any relationship to color.

Color Key shows what colors are used for what values, which could be distances or some other thing like B-factors.  If you start it from some other tool (Surface Color, Render by Attribute) the values will be the same thing that is shown in that other tool.

On Dec 22, 2010, at 2:17 AM, C.J. wrote:

> Dear Elaine,
> Thanks for explaining that for many times
> Regards!
> CJ
> 2010/12/22 Elaine Meng <meng at cgl.ucsf.edu>:
>> Hi CJ,
>> My previous reply (12/18 below) already explained how to change the units in the color key.  I can' t think of any other way to explain this, sorry.  If your structure is from the PDB, however, it is already in angstrom units.
>> Elaine
>> On Dec 20, 2010, at 7:44 PM, C.J. wrote:
>>> Thanks, but can I change the distance unit of color key in Chimera? Or
>>> I have to modify the pdb structure file to change that?
>>> 2010/12/18 Elaine Meng <meng at cgl.ucsf.edu>:
>>>> Hi CJ,
>>>> If you know what distance units are in your structure, you can simply apply the conversion factor to the values in the Color Key dialog.  In other words, if your structure is in nanometer units, you can just manually type new values into the Color Key dialog that are 10x the values that were there initially.  If the values from the structure are 10 and 50 (nanometers), you can just manually edit the values in the Color Key dialog to 100 and 500, then they will be in angstroms.  If your structure is in grid units where the grid points are spaced 1.582 angstroms apart, then you would multiply by 1.582 instead.  (etc.)
>>>> Best,
>>>> Elaine
>>>> -----
>>>> Elaine C. Meng, Ph.D.
>>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>>>> Department of Pharmaceutical Chemistry
>>>> University of California, San Francisco
>>>> On Dec 16, 2010, at 5:17 PM, C.J. wrote:
>>>>> Dear Dr. Elaine,
>>>>> I am afraid that my structure is not in angstrom coordinates.
>>>>> So, any way to change the color key?
>>>>> Thanks all the same.
>>>>> 2010/12/17 Elaine Meng <meng at cgl.ucsf.edu>:
>>>>>> Hi CJ,
>>>>>> If your structure and/or map data is in angstrom cooordinates, and you are coloring by distance in Surface Color, and you start Color Key from the button in Surface Color, it is already automatically in angstrom units.
>>>>>> Elaine

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