On 2004-10-22 (08:51) Dan Bolser wrote: >On Thu, 21 Oct 2004, timothy driscoll wrote: > >> >>1. choose from among four different gradient styles (rainbow, >>blue-white-red, black-white, or white-black). >> >>2. create gradients that apply to a single chain, span multiple >>chains, or apply separately to each chain of a multi-chain >>structure. up to four chains are supported at this time. >> >> >>Color Gradients is comptible with Jmol, Rasmol, and Chime, and is >>available here: >> >><http://www.molvisions.com/resources/color_gradients/> >> >> > >This looks really great. One thing I expected was that the gradient >would be 'squashed' to fit the length of the selection, so I would >always see one blue, one white and one red even if I only selected >three residues. Selecting around 40 residues I only see (a very >nice:) gradient from white to red. >
hi Dan, thanks. the algorithms for generating the color codes still need some testing; for example, it *was* my intention that you should get one blue, one white, and one red if you enter a stretch of three residues. :-) I'll have to take a closer look at optimizing that particular calculation. >One other thing I spotted using the grayscale was the following >color "color [255,-0,0]", which rasmol doesn't like. > excellent; good catch. can you tell me the range of residues you used to see a value of -0? >I was attempting to build something vaguely similar (in concept) >with the 'pdbHighlight' project, basically a resource for visually >annotating PDB files. Although I haven't found time to make my perl >scripts into a CGI page yet. > >http://bioinformatics.org/pdbHighlight/ > >This has been a work in progress for a couple of years ;) > looks like your goals are much more lofty than my own! I just wanted to recreate and improve the Rasmol 'color group' command. >One thing I would love to see is if you could 'serve' your scripts >as a web service with an API, then rasmol / jmol / chime could be >configured to lookup the results of that web service on a certain >command (i.e. based on a config file which would expand the language >syntax). The only practical difference with this approach is that it >avoids the need to copy / paste from one platform to another, but it >also opens up the possibility of sending all kinds of cool commands >to peoples molecular viewers on request. > interesting idea. I do plan to add a Jmol viewer to the output, so you can see the results of the gradient immediately, and a method to download the script file directly instead of copy-pasting. that might serve as an intermediate step... regards, tim -- Timothy Driscoll molvisions - see, grasp, learn. <http://www.molvisions.com/> usa:north carolina:wake forest ------------------------------------------------------- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
