Re: [PyMOL] rotate translate two different objects indpendently and legend

Hi Christian,

> I have a two chain protein and I want translat and rotate it using the
> commands translate and rotate. It is complicate to choose the rigth angel,
> because I cannot see the rotation axis. Is there a way to draw the axis system
> for the objects to see around which axis and how much I must rotate every
> single object. Does every object have is own axis system or is there a common
> system for all objects?

See http://www.pymolwiki.org/index.php/Axes.

Each object has its own transformation matrix. Rotate and translate
can act upon that matrix. See
http://www.pymolwiki.org/index.php/Get_object_matrix.


> When I color my protein according to the B-values is it possible to include a
> kind of  a legend like for the elctrostatics when I use APBS to get an idea
> about the minimum and maximum value?

An easy way is the following, but has two problems: (1) you're not
ensured the correct 1-1 mapping; (2) when you adjust the ramp the
lines colors don't change. But, it does work:

# fetch an example protein

fetch 1foo, async=0

# color it by b-factor

spectrum b, rainbow

# get the list of b-factors

x = []

cmd.iterate("1foo", "x.append(b)", space={'x':x})

# create the ramp across the range

cmd.ramp_new("myRamp", "1foo", [min(x), max(x)], "rainbow")


If I can recall the other way of mapping the ramp color to the lines,
I'll let you know. Right now it escapes me.

Cheers,

-- Jason

> Thanks in advance and Best Regards
>
> Christian
>
>
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120