Hi Yeping,
the spectrum command has a byres argument to operate on the residue level:
PyMOLspectrum 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:
PyMOLrun path/to/spectrumany.py
PyMOLspectrumany 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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