On Thu, 21 Oct 2004, timothy driscoll wrote: >hello, > >I have created a new resource for Jmol, Rasmol, and Chime developers >called Color Gradients. you can use it to create script commands that >apply a gradient color scheme to your molecule of choice. this is >similar to the 'color group' command already present in Rasmol, but with >some improvements: > >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/> > > >(you can also access it under the Resources menu at my home page, ><http://www.molvisions.com/>.) it will run in any Web browser; not even >javascript is required. ;-) > >to use Color Gradients, you will need to enter the chain designators, >and the starting and ending residue numbers for each chain. the output >is a simple html file containing your script commands, from which you >can select all, copy, and paste into your spt file (or an empty text >file). > >plans for the future include allowing a pdb file to be uploaded >directly, to read chains and residues from the file itself, and other >output and command formatting options. > > >if anyone has any suggestions for improving this resource, or if it >doesn't work as expected, please feel free to send me email (offlist, if >you prefer).
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. One other thing I spotted using the grayscale was the following color "color [255,-0,0]", which rasmol doesn't like. 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 ;) 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. Cheers, Dan. > > >regards, > >tim > ------------------------------------------------------- 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
