Re: [PyMOL] sticks

[Thomas H. <sp...@us...>]

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 <ahm...@gm...> 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