Re: [PyMOL] color each polymer chain differently

[Thomas H. <tho...@sc...>]

Hi Chandan,

in Incentive PyMOL 1.6 you can use the spectrum command to color by chain (will be enumerated) or by residue number. http://pymolwiki.org/index.php/Spectrum

In open-source PyMOL, you could use the spectrumany script to color by residue number: http://pymolwiki.org/index.php/Spectrumany

Cheers,
  Thomas

On 13 Mar 2014, at 03:19, Chandan Choudhury <ii...@gm...> wrote:
> On Thu, Mar 13, 2014 at 10:21 AM, Jordan Willis <jwi...@gm...> wrote:
> I think...
> 
> What is happening is that the color command should take in a name like “color yellow, i. 1" or a CMYK color vector. When you are saying “color 1” it is just starting at the first index of CMYK which is black.
> 
> There is a command for your problem though. Just say util.color_chains() and it will color all individual chains a different color.
>  
> Thanks Jordon for the reply. 
> 
> I tried using util.color_chains(). It colors differently upto chain no. 26. After 26 all the chains are of same color, as I donot have chain no after that.
> Some utility which can color by residue number would be very useful.
> 
> Chandan
> 
> On Mar 12, 2014, at 11:15 PM, Chandan Choudhury <ii...@gm...> wrote:
> 
> > Dear PyMOL users,
> >
> > I build 100 chains of polymer in a box. Residue number is different for every chain. Chain 1 hasresidue no. 1, chain 2 has residue no. 2 and so on. I want to color each chain differently.
> > So, I wrote a script which generates a pml file, and opening this pml file with PyMOL should color each chain differently.
> >
> > ##color.pml
> > load 128md_c.pdb
> > select 1, i. 1
> > color  1, i. 1
> > select 2, i. 2
> > color  2, i. 2
> > select 3, i. 3
> > color  3, i. 3
> > select 4, i. 4
> > color  4, i. 4
> > select 5, i. 5
> > color  5, i. 5
> > select 6, i. 6
> > color  6, i. 6
> > select 7, i. 7
> > ...
> > ...
> > color  125, i. 125
> > select 126, i. 126
> > color  126, i. 126
> > select 127, i. 127
> > color  127, i. 127
> > select 128, i. 128
> > color  128, i. 128
> >
> > I have 128 chains.
> >
> > What I find that mostly green or black dominates the coloring.
> > While displaying color by the numeric code, what is the maximum no, after which the color repeats?
> >
> > Chandan
> >
> > --
> > Chandan Kumar Choudhury
> > National Chemical Laboratory, Pune
> > India

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.