Hi Chandan -
It seems like you're being limited by the 26 numbered colors in the util.cbc
function. You could create your own randomized list of evenly-spaced colors,
something like the following (untested, but should be approximately
usable--sorry, I'm away from my computer today):
from pymol import cmd
from random import shuffle
my_colors = []
# 5^3 > 100
for i in range (0, 5):
r = 0.25 * i
for j in range (0, 5):
g = 0.25 * j
for k in range (0, 5):
b = 0.25 * k
my_colors.append([r, g, b])
# randomize list
shuffle(my_colors)
# color your chains
for x, c in enumerate(my_chain_list):
cmd.color(my_colors[x], c)
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Kong Lab
NYU Medical Center
kong.med.nyu.edu
212-263-7898
Sent from my iPhone
> On Mar 17, 2014, at 8:37 AM, "Thomas Holder" <thomas.hol...@schrodinger.com>
> wrote:
>
> 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 <iitd...@gmail.com> wrote:
>> On Thu, Mar 13, 2014 at 10:21 AM, Jordan Willis <jwillis0...@gmail.com>
>> 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 <iitd...@gmail.com> 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.
>
>
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