Hi Ahmet, On 22 Dec 2013, at 12:17, Ahmet yıldırım wrote: > Pymol show them as a sticks but they are very similar. How can I color each > residue with different colors?
if you have incentive PyMOL 1.6, you can use the spectrum command to color by residue type: PyMOL> spectrum resn With older versions or with open-source, you have to do this manually: PyMOL> color blue, resn ALA PyMOL> color red, resn GLY PyMOL> color yellow, resn CYS PyMOL> ... There are scripts on the web for that, for example Robert Campbell has one: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ Hope that helps. Cheers, Thomas On 22 Dec 2013, at 12:17, Ahmet yıldırım <[email protected]> wrote: > Dear Thomas, > > I did as you said "PyMOL> set use_shaders, 0". The problem is solved. Thanks. > But I have a small problem. > I typed: > select resi resi 15-18 > show sticks, sele > > Pymol show them as a sticks but they are very similar. How can I color each > residue with different colors? > > Thanks in advance > > 2013/12/22 Thomas Holder > Hi Ahmet, > > could be a shader problem (missing support by your graphics driver). Try: > > PyMOL> set cylinder_shader_ff_workaround > (see http://pymolwiki.org/index.php/Cylinder_shader_ff_workaround ) > > or: > > PyMOL> set use_shaders, 0 > > Cheers, > Thomas > > On 22 Dec 2013, at 00:39, Ahmet yıldırım wrote: > > > Dear users, > > > > I want to show the residue 15 as a stick in xxxx.pdb. > > pymol-->file-->Open-->xxxx.pdb > > PyMOL> hide everything, all > > PyMOL> select active, resi 15 > > PyMOL> show sticks, resi 15 > > > > Unfortunately, pymol doesnt show it as a stick. Please see image > > https://www.dropbox.com/s/24gz1kcathiu2x6/resi-15.png > > Where did I mistake? > > > > Thanks in advance > > > > -- > > Ahmet Yıldırım > -- > Ahmet Yıldırım ------------------------------------------------------------------------------ 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 ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
