Re: [PyMOL] color each polymer chain differently
Hi Chandan - Back in the lab today. I took a look at the code I sent and realized that one can’t simply pass a tuple to cmd.color(), as it only accepts named colors, so you have to use cmd.set_color(). So here (below) is a modified, fleshed-out version of what I sent yesterday, with the protein components of the T. thermophilus ribosome asymmetric unit (110 chains) as an example. For a larger number of colors, you would simply have to increase the ranges for i, j, and k in the loop that creates the RGB tuples. Some of the colors turn out to be fairly similar (e.g. those differing by only one RGB component), so also maybe check out, e.g., this SO question and its answers for alternative approaches: http://stackoverflow.com/questions/470690/how-to-automatically-generate-n-distinct-colors. Cheers, Jared ### from pymol import cmd from random import shuffle cmd.fetch(2wdk, async=0) cmd.fetch(2wdl, async=0) cmd.fetch(2wdm, async=0) cmd.fetch(2wdn, async=0) # remove non-polymer components so we can just view the cartoon cmd.remove(all and not polymer) # remove RNA chains to get a better view of individual protein chains cmd.remove(chain A) my_chains = [] for obj in cmd.get_names(): for ch in cmd.get_chains(obj): my_chains.append((obj, ch)) print There are currently %s chains to be colored. % len(my_chains) 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 (optional) shuffle(my_colors) print shuffled the colors # name the colors for i, tup in enumerate(my_colors): cmd.set_color(mycolor_%s % i, %s % tup) print set color mycolor_%s to %s % (i, tup) # color your chains for i, ch in enumerate(my_chains): sel = %s and chain %s % (ch[0], ch[1]) color = mycolor_%s % i color_tuple = my_colors[i] print %s will be colored %s (%s) % (sel, color, color_tuple) cmd.color(%s % color, sel) ### -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Mar 17, 2014, at 2:07 PM, Sampson, Jared jared.samp...@nyumc.orgmailto:jared.samp...@nyumc.org wrote: 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.eduhttp://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
Re: [PyMOL] color each polymer chain differently
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
Re: [PyMOL] color each polymer chain differently
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:
Re: [PyMOL] color each polymer chain differently
On Thu, Mar 13, 2014 at 10:21 AM, Jordan Willis jwillis0...@gmail.comwrote: 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 has residue 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 pmlfile 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 -- 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 -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- 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
[PyMOL] color each polymer chain differently
Dear PyMOL users, I build 100 chains of polymer in a box. Residue number is different for every chain. Chain 1 has residue 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 -- 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
Re: [PyMOL] color each polymer chain differently
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. 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 has residue 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 -- 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 -- 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
