Gunnar Vikberg wrote: >Dear Tim Driscoll and JMol Dev List, > > > >>>What should the command be called? >>>---------------------------------- >>> >>>If this is a script command to create bonds then it seems that it >>>should >>>be called 'bond' ... the verb bond. >>> >>>Then again, the other script commands are called 'spacefill' and >>>'wireframe', not 'atom' and 'bond'. This has the advantage in that >>>there >>>is not confusion between the command name and the abstract concept/ >>>object. >>> >>>Q: Thoughts on script command name? Do you like 'bond' or 'link' or >>>something else? >>> >>> >>link is not bad. how about connect? or join? >> > >I'd be a little cautious when using the CONNECT word for a command in Jmol. >I'm not >sure where I've seen it before, but if I'm correct, PDB files can use the >CONNECT >keyword to create a connection between atoms that might not be bonded >otherwise. I >prefer the term LINK, JOIN or BOND. > > Isn't that exactly what the new command is supposed to do: "create a connection between atoms that might not be bonded otherwise" ? Therefore I think "connect" would be a very good choice because it is already used for the same purpose. >>>How are atoms specified? >>>------------------------ >>> >>>The 'monitor' command in rasmol takes atom numbers as arguments. I >>>don't >>>like this. >>> >>> >>why not? atom numbers, while not entirely unique, are closer to >>unique than anything else. and I do like Eric's idea of being able >>to use xyz coordinates as an alternate syntax. >> > >I do agree with Tim on this one. Atom numbers can also be "renumbered" as to >make >them unique, therefore having a perfectly viable method of selecting individual >atoms. Nevertheless, many people I've worked with in the past do get confused >with >that command, so something more specific, that means something to people, >would work >better. > > I don't think that Miguels proposition of using atom expressions contradicts your wish to use atom numbers. It includes it (with a slightly different syntax) and it would make the command much more powerful. I would like that!
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