Indraneel, PyMOL's cartoon generation code is some of the worst "production" code I have ever written in my life. It consists of one huge 2,000 line function with numerous one or two-letter variables and all kinds of implicit assumptions about the linear structure of the protein and the discrete nature of secondary structure elements. It would requires tremendous effort to make changes to it safely, and as such, it serves as a classic example of how NOT to write important code. [layer2/RepCartoon.c, RepCartoonNew()]
My only defense for that mess it is that it has performed extraordinarily well over a period of years with all kinds of structures, from small peptides up to million-atom virus particles. Despite is ugliness, is fast, stable, and functional. Eventually it will be overhauled and we'll probably switch over nicer looking to Bezier curves at that point -- but until then, I am loath to make any significant modifications to it. Since PyMOL is open-source you are welcome to try, but I think your time would be better spent constructing an alternate implementation that meets your specific needs. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Indraneel Majumdar > Sent: Saturday, November 05, 2005 7:29 PM > To: pymol-users@lists.sourceforge.net > Cc: Warren DeLano > Subject: [PyMOL] Discreet cartoon representation for > overlapping secondary structure ? > > Hi, > > Is changing cartoon representation a major work? My program > PALSSE defines overlapping Secondary Structural Elements and > it would be nice if I could see cartoons without having > consecutive elements merged. > > It is technically possible for consecutive helices or > consecutive strands or helices and strands to have upto 2 > common residues. > > I was wondering if the start and ends could somehow be > distinguished, eg. by changing or adding another "more_fancy" > option to not remove the head arrow of any SSE (also add > arrow to helices) and modify the base of all SSE so they are > visible at all times (probably show the base as a circle?). > The SS merge feature would probably have to be switched off > before this though. > > Which is the best place to start modifications? > > An example arrow: > > __ * > * * * * > * ***************** * > * * > * ***************** * > * __ * * * > * > > 1 2 3 4 > > The head should be visible even if 1-2 overlaps on 3-4. > > > Thanks, > Indraneel > > -- > http://prodata.swmed.edu > > > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App > Server. Download > it for free - -and be entered to win a 42" plasma tv or your very own > Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
