> Quoting Miguel <[EMAIL PROTECTED]>: > >> It is not clear to me where you want to take this disussion. >> > I started this discussion to help us to decide what we should > use for highlighting boundaries between two amino > acids: 'pmesh' or 'pseudo atoms + bonds'.
Please be patient with me. Remember that I am not a chemist and do not understand anything about the applications that you are trying to build. I have no idea what the 'boundary between two amino acids' is. All I understood was 'can I put a label on a pmesh'? > With the current state of Jmol we could only use pmesh > combined with a pseudo atom for labelling. Therefore we > would most probably use 'pseudo atoms + bonds' although the > highlighting wouldn't be as good as with 'pmesh'. I am getting confused. > Because I don't want to force adding features for 'misusing' > bonds I didn't went further in that direction. Good. I do not like to misuse features. > If pmesh labelling would be added we would presumably > use 'pmesh', even with a lot of different files. But this sounds like you would be misusing the pmesh command > I like Timothy's idea of a new annotation object best, because > it would make any precomputing and/or changing of the PDB files > unnecessary. Tim wrote: >> it seems to me that it might be simpler to add a new kind of >> annotation object (like a label, but a filled rectangular cube). i.e., >> >> set blocksize 12 >> color blocks red >> block aa3,aa4 > But I guess it would be more work than adding a lablling > command for 'pmesh'. I am in favor of adding features if they are generally useful. We need to restart this discussion from the beginning. Draw me a picture of what you want. Use a graphics program or use a pencil & paper and scan the results. Tim sent me this url: http://www.expasy.org/cgi-bin/prosite/PSView.cgi?ac=PS50020&onebyarch=1&hscale=0.6 But I do not understand how this relates to your request. Miguel ------------------------------------------------------- This SF.Net email is sponsored by: Power Architecture Resource Center: Free content, downloads, discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
