Dear Jared,Thank you for the reply. But I still have a couple of questions:
As for the spectrumbar script, how could I assign a particular data value
to a particular color? By using the command:spectrumbar blue, white, redI can
get a spectrumbar. If the range of my data is -0.3~2.3, maybe I can label two
end of the bar with -0.3 and 2.3 manually, respectively. But if I want to label
more data to the bar? How shold I do?
As you suggest, I can simplely get a 2D box with a linear gradient fill.
But the question is the same with above: how could I correctly label the bar
according my data set?Best regards,
Yeping------------------------------------------------------------------
发件人：Sampson, Jared <jared.samp...@nyumc.org>
发送时间：2014年4月29日(星期二) 04:36
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 b-factor colum
Hi Yeping -
I was about to suggest Sean Law’s new 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 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 <sunyep...@aliyun.com> 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:
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 <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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