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. >> 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. >> We already have a very flexible and powerful mechanism for specifying >> atoms. Atom expressions allow us to select atom sets based upon a >> number >> of characteristics. >> >> The 'link' command should use atom sets to specify the atoms. >> > perhaps I'm confused, but what would be the end use of the link > command? I thought it would be used to add a single connection, say > for illustrative purposes. in this case, I would vote for a simple > mechanism similar to the current monitor command. but then, I am > certainly open to being convinced otherwise. What would the atom sets in the LINK command look like? It might end up being a little more confusing than the rasmol monitor command, but surely will work correctly with files that may not be properly numbered. Regards, Gunnar Vikberg ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnk&kid3432&bid#0486&dat1642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
