Angel Herraez wrote:
>I am testing the new 11.1.30 with PQR file (made with pdb2pqr)
>The file loads Ok, now I want to color atoms by partial charge.
>
>I'm following clues from 2 former messages by Bob: how to color by
>occupancy, using a custom-defined property, and a mention of
>properties read from pqr files ("radius is property vanderwaals,
>charge is property partialcharge").
>So I have tried these two methods:
>
>1)
>propertyColorScheme = "rwb"
>color partialcharge
>
>
>
>2)
>x = {*}.partialcharge.all
>propertyColorScheme = "rwb"
>data "property_ch @x"
>color atoms property_ch
>
>And I get similar but different tints of color. Since this is a
>protein, I cannot check beforehand which is the correct way of
>reading charge data.
>Help?
>
>
>
Well, I can see lots of people are going to find this useful. That's great.
There are two distinct methods of coloring by properties now. The old
way includes:
color atoms partialcharge
color atoms formalcharge
color atoms fixedTemperature
color atoms relativeTemperature
You can still use these, but now we also have
color atoms property partialcharge
color atoms property formalcharge
color atoms property temperature
color atoms property (many others)
color atoms property_xxx (custom user property)
Looking at the code, I see this comment regarding the old way:
// This code assumes that the range of partial charges is [-1, 1].
So what you are seeing is that in this case the charges are not -1 to 1;
The newer method makes no such assumption, and so it colors them from
whatever
their minimum value is to whatever their maximum value is. The old way
is better, because
it allows for more consistent comparisons across different models.
I just added a way of setting the range to whatever you want:
color atoms property_x absolute -3.0 3.0
so then the absolute range -3 to 3 is used across the full spectrum
instead of basing
the color range on the range of values in the dataset.
so now
color atoms partialcharge
will be the same as
color atoms property partialcharge absolute -1.0 1.0
This is like the isosurface "color absolute -1.0 1.0" idea.
Bob
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