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
