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[PyMOL] RE： gradually changed colors with b-factor colum
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From: sunyeping <sun...@al...> - 2014-04-29 02:21:03
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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 <Jar...@ny...> 发送时间：2014年4月29日(星期二) 04:36 收件人：孙业平 <sun...@al...> 抄 送：pymol-users <pym...@li...> 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 <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: 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 ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. 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