[PyMOL] gradually changed colors with b-factor colum

[sunyeping <sun...@al...>]

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: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.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...>
发送时间：2013年12月11日(星期三) 12:49
收件人：孙业平 <sun...@al...>
抄　送：pymol-users <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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