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. > > > ------------------------------------------------------------------------------ > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and their > applications. Written by three acclaimed leaders in the field, > this first edition is now available. Download your free book today! > http://p.sf.net/sfu/13534_NeoTech > _______________________________________________ > 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 ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech _______________________________________________ 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