at 1:55 pm EDT on (Tuesday) 18 November 2003 Miguel said: > >>> one can write a javascript method for finding most of this, using > >>> 'show pdbheader' in Chime, but what a pain. maybe JMol can have a > >>> suite of 'show info' commands to access structure data like this? > > >> Writing code to parse the text output would be a disaster. > >> > > not sure I follow; can you explain? > > I was just agreeing with you ... it would be a disaster to have to > parse the text output of Âshow pdbheader in JavaScript. > > The Âdisaster was for you to have to do the work ... not for me to do > it :-) > ah, yes. phew.
> > I'm talking about making common current properties available as > > discrete elements - for example, show sequence, show ligand, show > > resolution. some of these are already implemented in other apps - > > show sequence, view show, show info. most of the rest is only > > accessible via show pdbheader. > > I understand and agree. These pieces of data should be available as > individual data elements. > > In general, I would lean towards making them Âproperties of the > molecule rather than providing individual commands for each data value. > *But* if there already is a Âstandard established by other programs > then we should make that available. > I can think of a handful of 'show...' commands built into the RasMol/Chime command language. I use most of them one way or another, but I don't like the way they work (my two cents, of course). they are not consistent, so I have to write a different method to handle output from each command. yuck. I heartily agree that making structure info available as properties is the way to go, with token suport for backwards compatibility. I, for one, would rewrite my own code to access the atom properties directly rather than use the script commands. but that's just me. the info-gathering commands from existing apps are: show info[rmation] + returns String with some basic info about the file. show pdbheader + returns String with the entire pdb file header. view show user + returns String with the current translate and rotate settings. view show + returns String with position of structure as: "view set Xrot Yrot Zrot zoom xtrans ytrans ztrans slab cenX cenY cenZ" show selected + in the display, applies a gold color to all selected atoms. show sequence + returns String with the primary sequence, in 3-letter residue code. show symmetry + returns String with details of crystal space group and unit cell. someone please correct me if I have missed any. > > So, within existing applications, what do people do with PickCallBack? > I am building a quizzing application designed for mol vis Web sites. one of the question types is called 'picking', where a student must click on an atom in the 3D structure to answer the question (for example, click on the backbone of any polar amino acid). being able to access atom properties directly from pickcallback would be very helpful here. I have also used pickcallback to modify the currently selected set (i.e., add an atom, subtract an atom), make side chains visible when the alpha carbon is clicked, make various pieces of a structure disappear or change appearance, and more. :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest ------------------------------------------------------- This SF. Net email is sponsored by: GoToMyPC GoToMyPC is the fast, easy and secure way to access your computer from any Web browser or wireless device. Click here to Try it Free! https://www.gotomypc.com/tr/OSDN/AW/Q4_2003/t/g22lp?Target=mm/g22lp.tmpl _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
