Hi Yeping -
It doesn’t look like Spectrumbar supports additional labeling, but you could
add labels at each end by using pseudoatoms at the positions where you want the
labels to appear (see the second example at
http://pymolwiki.org/index.php/Pseudoatom).
For the 2D gradient box, you can create whatever intermediate labels you like,
just keep the same scale. For example, if your bar covers data values from
-0.3 to +2.3 and you make it 260 pixels wide, then each 10px accounts for 0.1
unit. So “0.0” will be 30px from the left side, “+0.5” will be at 80px, and so
forth. After you create it at that scale, you can resize it as you wish and
the relative positions will remain the same.
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Apr 28, 2014, at 10:20 PM, sunyeping
<sunyep...@aliyun.com<mailto:sunyep...@aliyun.com>> wrote:
Dear Jared,
Thank you for the reply. But I still have a couple of questions:
As for the spectrumbar<http://pymolwiki.org/index.php/Spectrumbar> script,
how could I assign a particular data value to a particular color? By using the
command:
spectrumbar blue, white, red
I 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<mailto: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<mailto:sunyep...@aliyun.com>>
抄 送：pymol-users
<pymol-users@lists.sourceforge.net<mailto: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<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
<sunyep...@aliyun.com<mailto: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:
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
<spel...@users.sourceforge.net<mailto: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<mailto:sunyep...@aliyun.com>>
抄 送：pymol-users
<pymol-users@lists.sourceforge.net<mailto: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<mailto: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<mailto: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<mailto:sunyep...@aliyun.com>>
> 抄 送：pymol-users
> <pymol-users@lists.sourceforge.net<mailto: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<mailto: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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