Re: [PyMOL] gradually changed colors with b-factor colum

[Sampson, J. <Jar...@ny...>]

Hi Yeping -

I was about to suggest Sean Law’s new spectrumbar<http://pymolwiki.org/index.php/Spectrumbar> script, but I see he beat me to it.  You’ll have to adjust the positioning of the bar with some trial and error.  Also, in case you get a “NameError: global name 're' is not defined” error, simply change the 4th line from:

    from re import *

to

    import re

I’ve just submitted a pull request<https://github.com/Pymol-Scripts/Pymol-script-repo/pull/55> with this fix, but if you download the script before it’s accepted, you'll have to make the change yourself.

Alternatively, you could fairly easily create a simple 2D box with a gradient fill in e.g. Inkscape or Illustrator with the appropriate colors and add the labels manually.  So long as you specify a linear gradient, it should be fairly consistent with the PyMOL values.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/


On Apr 27, 2014, at 8:50 AM, sunyeping <sun...@al...<mailto:sun...@al...>> wrote:

Dear proessor Holder and pymol users,

I previously tried to color a protein structure accord to a set of customer data. I replaced the b factor of individual Ca atoms and colored the structure with the command:

spectrum b, blue_white_red, byres=1

But I think I need a color scale bar to show the range of the data set. According to PymolWiki (http://www.pymolwiki.org/index.php/Advanced_Coloring#Creating_a_Color_bar), this can be done with the following steps:

  1.  Create a pdb-file which contains CA positions only, whereas the numbers correspond to your wanted increments of colors. Make CA's to be separated by 5 Angstroem.
  2.  Load this new pseudobar-pdb file into PyMOL, make bonds between increment 1 and increment 2 [increment 2 and increment 3 and so on...], define/assign a smooth color for each increment (copy colors definition from automatically created colors made by b-factor script) and show the b-factor bar as lines (or sticks).

Could you tell me how to assign blue_white_red color for these increment? And if the range of my data set is -0.8 to 2.3, how to make the color gradient reflect this range? Thank you very much.




Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences

------------------------------------------------------------------
发件人：Thomas Holder <sp...@us...<mailto:sp...@us...>>
发送时间：2013年12月11日(星期三) 12:49
收件人：孙业平 <sun...@al...<mailto:sun...@al...>>
抄　送：pymol-users <pym...@li...<mailto:pym...@li...>>
主　题：Re: [PyMOL] 答复： gradually changed colors with flexibility

Hi Yeping,

the spectrum command has a "byres" argument to operate on the residue level:

PyMOL>spectrum b, blue_white_red, byres=1

There is no white_blue color ramp, but there is a script which provides this:
http://pymolwiki.org/index.php/Spectrumany
It doesn't have the byres argument. If you only show cartoon, just limit the selection to CA atoms:

PyMOL>run path/to/spectrumany.py
PyMOL>spectrumany b, white blue, name CA

If you want to show all atoms, you can map the CA atom b-factor to all residue atoms with this script:
http://pymolwiki.org/index.php/AlphaToAll

Hope that helps.

Cheers,
Thomas

On 10 Dec 2013, at 01:04, sunyeping <sun...@al...> wrote:

> Hi, professor Holder,
>
> Thank you for the reply, but how can I do this on the level of individual amino acids in stead of atom? I have two homolog stuctures and I want to map the difference between the b factors of the corresonding residues of these two stuctures rather than individual atoms. And I want to use gradually deepened color from white to blue. Could you explain more in detail? Thanks.
>
> Yeping Sun
>
> Institute of Microbiology, Chinese Academy of Sciences
>
>
> ------------------------------------------------------------------
> 发件人：Thomas Holder <sp...@us...>
> 发送时间：2013年12月10日(星期二) 04:50
> 收件人：孙业平 <sun...@al...>
> 抄　送：pymol-users <pym...@li...>
> 主　题：Re: [PyMOL] gradually changed colors with flexibility
>
> Hi Yeping,
>
> use the spectrum command:
>
> PyMOL> spectrum b, blue_white_red
>
> http://pymolwiki.org/index.php/Spectrum
>
> Cheers,
> Thomas
>
> On 09 Dec 2013, at 11:30, sunyeping <sun...@al...> wrote:
>
> > Dear all,
> >
> > I want to show amino acids in a structure according to their flexibility (B factor) by gradually changed colors. Can pymol do this? Thanks.
> >
> > Yeping Sun
> >
> > Institute of Microbiology, Chinese Academy of Sciences

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