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 ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
