at 2:32 pm EDT on (Saturday) 15 November 2003 Miguel said: > > so if I select Glu134:B, > > for example, I would get an array with: > > > > number of atoms selected > > id of group selected > > number of selected group > > chain of selected group > > > > what other info is accessible? > Lots of things :-) > as a developer, I'd like access to all of it, please. :-)
> > could JMol tell me that I selected an > > atom in the ligand, for example? or the color? > Yes. > very nice! > Uhh ... in 25 words or less ... what is a ligand? > a small molecule that binds specifically to a larger one. many pdb files define the ligand in the pdb header; I thought JMol might be able to read that info if it exists. [...] > > What do you think about something like this: > > A selection set should allow you to enumerate all the atoms > in the set. (Or perhaps there is an iterator which always > enumerates the atoms in the currently selected set) > > Given each of these atoms you can inquire about its properties. > > Does that sound right? > that sounds excellent. > > for example, click on atomno=1738 in 1d66.pdb and Chime will return: > > > > Atom: O 1738 Hetero: HOH 343 Chain: B > > > > > > parsing this kind of string in javascript is a bit of a pain; again, > > as a developer, it would be much better to have this as a well-formed > > array instead. (see my comments above about select.) and it would be > > even better if the atom data included some state info - what color is > > it, how is it rendered... > > I think that the PickCallBack should pass you at atom object (or atom > ID). Using this, you should be able to get the properties of the atom. > exactly! > What does PickCallBack do if you rubber-band select a rectangle of > atoms in Chime? ( Or is this functionality not available? ) > not available. you can only pick single atoms on screen in Chime. as far as I know, likewise for Rasmol. > > I do wonder if JMol might be do a better job than either Chime or > > RasMol at returning well-formed data about the loaded structure. for > > example, all of this should be accessible info: > > > > the url > > the compound > > the organism > > if a crystal, the resolution > > the number of chains > > identity and chemical formula of any hetero groups > > the ligand > > the helices or sheets > > the primary sequence > > the current 3D position > > These should be properties of the current 'model' and should all be > accessible. > > > > 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'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. if this is a disaster to include in the code itself, maybe I (or someone) can write a javascript 'converter' to include with the distribution - a routine that parses the psbheader info. is that better? [...] > Down the road we will have the chance to define/build one or more 'Jmol > scripting langages' that are better suited for web application > development ... in JavaScript and/or PHP and/or Python and/or > something. But that is for the future. > ah, I see myself jumping the gun here, it's true. I'll try to file my "wouldn't it be great" requests for the future. :-) regards, :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
