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
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发件人：Thomas Holder <spel...@users.sourceforge.net>
发送时间：2013年12月11日(星期三) 12:49
收件人：孙业平 <sunyep...@aliyun.com>
抄 送：pymol-users <pymol-users@lists.sourceforge.net>
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 <sunyep...@aliyun.com> 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 <spel...@users.sourceforge.net>
> 发送时间：2013年12月10日(星期二) 04:50
> 收件人：孙业平 <sunyep...@aliyun.com>
> 抄 送：pymol-users <pymol-users@lists.sourceforge.net>
> 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 <sunyep...@aliyun.com> 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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