From: timothy d. <mol...@ma...> - 2003-11-15 10:53:44
|
at 9:37 am EDT on (Saturday) 15 November 2003 Miguel said: > Paul, > > Thanks very much for doing this investigation. > > > > > For more information on how the MessageCallback method works in Chime > > and why it can be usefull : > > - every command sent to chime is displayed by this function (when you > > set debug=true in the plugin parameters) > It is not clear to me exactly what you mean by 'command' in this context. > Do you mean that the text of every RasMol/Chime script statement is sent > through MessageCallBack? > yes. > What happens if 'debug=false' is set? > only the return from Chime is available, not the command sent to Chime. > > - when a selection is done, the number of atom selected is displayed > Is this just the count of selected atoms? > Is there any text or identifier that says it was a selection? > in Chime, a 'select' command returns a string through MessageCallBack: 156 atoms selected! it always contains "atoms selected!" in JMol, maybe a select command could return an array instead of a string? 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? could JMol tell me that I selected an atom in the ligand, for example? or the color? I guess I'd like to have all of the Atom properties accessible - but I bet that is a chore ;-) maybe some middle ground though... > > - when an atom is clicked, its references are given > This sounds very similar to PickCallBack ... none of this is implemented yet. > > What do the atom 'references' look like? > 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... > > - show chain, show model, show information, show pdbheader, show > > sequence, show view, send a message back to the user via this method. > As I recall, none of the 'show' commands are currently implemented. It > won't be difficult to do, but it hasn't happened yet. > > Is the output of these commands in Chime the same as in RasMol? > I don't know, sorry. 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 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? sorry for piling on, but I'm salivating at the prospect of having all of this data, well-formed and ready to use. > > As > > Tim told, these functions are very usefull in dynamics web sites. > > In the following page by Eric Martz, you can see how this works in > > Chime. > > > http://www.umass.edu/microbio/chime/chimehow/fs_cmdln.htm > IIRC, if you send a long script to Chime, the messages returning are scrambled (IOW, not in the same order as they went to Chime). I don't recall the details, and maybe this has no bearing on JMol - maybe Paul can say more? regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest |