Re: [ccp4bb] atomic coloring for the color blind
How about Braille for those who are blind to all colours? -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] atomic coloring for the color blind
David, Do you know of a program to make accurate braille representations of an electron density map :) That would be cool. Maybe in the future [See: http://www.wired.com/wiredscience/2012/08/smart-fingertips-virtual-senses/ http://www.ethlife.ethz.ch/archive_articles/100816_virtuelle_realitaet_cho/index_EN and http://www.technologyreview.com/news/428736/disney-researchers-add-virtual-touch-to-the-real-world/] For the really hard core scientist (this is a little creepy): http://io9.com/5846275/biotech-breakthrough-monkeys-can-feel-virtual-objects-using-a-brain-implant Food for thought, Steve sherron_...@yahoo.com On 6/1/2013 12:16 PM, David Schuller wrote: How about Braille for those who are blind to all colours?
[ccp4bb] atomic coloring for the color blind
I feel badly that one of my undergrads had trouble telling an O from a C in a pymol homework set because he's color blind. (The assignment involved telling me why the a GTP analog (GDPCP) wasn't hydrolyzed). Is there a handy by-atom coloring scheme I can recommend that works for the red-green color blind? thanks, Professor Rice ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edumailto:pr...@uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp
Re: [ccp4bb] atomic coloring for the color blind
Why not use yellow carbons (colour by atom menu) and hit the builder button in pymol which shows bond order (carbonyls). You could also type colour gray, name o, this colours the carbonyls gray (or any other colour that works) name o* colours all oxygens Hope this helps From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phoebe A. Rice Sent: Friday, 31 May 2013 1:35 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] atomic coloring for the color blind I feel badly that one of my undergrads had trouble telling an O from a C in a pymol homework set because he's color blind. (The assignment involved telling me why the a GTP analog (GDPCP) wasn't hydrolyzed). Is there a handy by-atom coloring scheme I can recommend that works for the red-green color blind? thanks, Professor Rice ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edumailto:pr...@uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp
Re: [ccp4bb] atomic coloring for the color blind
On Friday, May 31, 2013 01:34:51 pm Phoebe A. Rice wrote: I feel badly that one of my undergrads had trouble telling an O from a C in a pymol homework set because he's color blind. (The assignment involved telling me why the a GTP analog (GDPCP) wasn't hydrolyzed). Is there a handy by-atom coloring scheme I can recommend that works for the red-green color blind? Phoebe: Here is the podo color palette recommended as being distinguishable by both protanopic and deuteranopic color-blind viewers. The down side is that this is is a more stringent restriction than accommodating red/green color defects alone, and makes the colors less distinct for normal-vision viewers % # This file is distributed as part of gnuplot. # Palette of colors selected to be easily distinguishable by # color-blind individuals with either protanopia or deuteranopia # Bang Wong [2011] Nature Methods 8, 441. set linetype 1 lc rgb black set linetype 2 lc rgb #e69f00 set linetype 3 lc rgb #56b4e9 set linetype 4 lc rgb #009e73 set linetype 5 lc rgb #f0e442 set linetype 6 lc rgb #0072b2 set linetype 7 lc rgb #d55e00 set linetype 8 lc rgb #cc79a7 set linetype cycle 8 % Translating these colors to atom types is another question, however. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] atomic coloring for the color blind
Professor Rice, When publishing in NAR (Nucleic Acids Research), it was recommended that we use colors friendly to the color blind. You can read about it here: http://jfly.iam.u-tokyo.ac.jp/html/color_blind/ It is quite nice that they went to the trouble of showing us how they see it. And there are plenty of suggestions how to do better. In fact, it turns out that you need not stay away from red and green, but define them somewhat different and it will work better. Ever since I made all my illustrations like this once, I try to do it every time, for any journal, just in case. I consult this page often, it is quite helpful to me. See especially near the bottom of the page colors unambiguous both to color-blinds and non-color-blinds. Hope this helps you too. Mark -Original Message- From: Phoebe A. Rice pr...@uchicago.edu To: CCP4BB CCP4BB@JISCMAIL.AC.UK Sent: Fri, May 31, 2013 2:35 pm Subject: [ccp4bb] atomic coloring for the color blind I feel badly that one of my undergrads had trouble telling an O from a C in a pymol homework set because he's color blind. (The assignment involved telling me why the a GTP analog (GDPCP) wasn't hydrolyzed). Is there a handy by-atom coloring scheme I can recommend that works for the red-green color blind? thanks, Professor Rice ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp
Re: [ccp4bb] atomic coloring for the color blind
FYI Kevin Cowtan has a web page that discusses using color diagrams with respect to the color blind interpretation. http://www.ysbl.york.ac.uk/~cowtan/colour/colour.html -Bryan
Re: [ccp4bb] atomic coloring for the color blind
Phoebe, I'm red green blind myself, and it is not as straight forward as it sounds. The problem is that we see red and green despite lacking one of the color receptors (I actually prepared a figure using red and green once and got a referee comment that red/green blind people would have difficulties with - which I could attest to being wrong...). We can distinguish between bright green and bright red! But in between, things are sketchy. Our brains learned to associate certain gray levels with either green or red (e.g. on our old BW TV, I did see all the grass as green, I was flabbergasted at the age of 6 to learn that our neighbor did not see the colors in our BW TV; Also, I called one of my class mates in junior high on his ugly green jeans, only to learn they were washed out black). My advice: Convert the image to gray scales. If you can't tell the difference, people with color seeing problems can't tell them apart. Actually, chose your color scheme so it gives good contrast in a gray scale image. This also should take care of the much rarer blue deficiency; and it might cut down on reproduction cost - as everything should be reproducible on a BW copy machine. HTH, Jens I feel badly that one of my undergrads had trouble telling an O from a C in a pymol homework set because he's color blind. (The assignment involved telling me why the a GTP analog (GDPCP) wasn't hydrolyzed). Is there a handy by-atom coloring scheme I can recommend that works for the red-green color blind? thanks, Professor Rice ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edumailto:pr...@uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp
