[PyMOL] gradually changed colors with flexibility
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 -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631&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
[PyMOL] Sphere_scale vs Dot_scale
I can show an atom as a sphere, and then scale that sphere to 0.5. I can show an atom as dots, but then cannot scale the volume of those “dots” to 0.5. There is no dot_scale command in PyMOL. Is there anyway to scale the volume of the dots in some way? H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631&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
Re: [PyMOL] Sphere_scale vs Dot_scale
Hi Adam, alter all, vdw*=0.5 rebuild Cheers, Thomas On 09 Dec 2013, at 14:51, H. Adam Steinberg wrote: > I can show an atom as a sphere, and then scale that sphere to 0.5. > I can show an atom as dots, but then cannot scale the volume of those “dots” > to 0.5. There is no dot_scale command in PyMOL. > > Is there anyway to scale the volume of the dots in some way? > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631&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
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 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 -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631&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
Re: [PyMOL] Sphere_scale vs Dot_scale
Works perfectly! Thank you so much! On Dec 9, 2013, at 2:43 PM, Thomas Holder wrote: > Hi Adam, > > alter all, vdw*=0.5 > rebuild > > Cheers, > Thomas > > On 09 Dec 2013, at 14:51, H. Adam Steinberg > wrote: > >> I can show an atom as a sphere, and then scale that sphere to 0.5. >> I can show an atom as dots, but then cannot scale the volume of those “dots” >> to 0.5. There is no dot_scale command in PyMOL. >> >> Is there anyway to scale the volume of the dots in some way? >> >> H. Adam Steinberg >> 7904 Bowman Rd >> Lodi, WI 53555 >> 608/592-2366 H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631&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
[PyMOL] 答复： gradually changed colors with flexibility
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 发送时间：2013年12月10日(星期二) 04:50 收件人：孙业平 抄 送：pymol-users 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 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 -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631&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-- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631&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
