Jan wrote: >>>> Q: Should this 'moving to the unitcell box' be automatic >>>> at load time, or under user command?
> only under user command. OK >>>> Let's look at two examples: >>>> >>>> 3CRO.pdb has the asymmetric unit outside the unitcell cage. Does >>>> anyone ever want to see it that way? >>> >>> >> >>No, one unit cell, P1, while possibly, this is a clear situation where >> it should be translated... especially, because it is just one unit >> cell, and it clearly cannot display (without unit cell duplication by >> Jmol itself) any interactions with molecules from surrounding unit >> cell. >> >> > even after translation of the unitcell to contain 3cro it is not packed. > May be it was better to start with the PDB file definition and move the > unit cell cage only after the first > "pack unitcell" > command, when the unitcell gets packed? I think that Jan is saying that it should start off outside the unitcell. >>>> To pack things into the unitcell cage the user is going to have to >>>> send a script command which will do the packing. >>> >>> >> >>Yes, that's perfect as a backup option. >> >> > I prefer this to be an command that has to be explicitly called by the > script. OK >>>>> > Once we have symmetry operations available too, we can apply >>>>> these by scripting too... combine this with selecting one >>>>> molecule from the unit cell ... >>>> >>>> > in e.g. 1gu8 they mentioned an SYMOP which may be useful to address > specific symmetry operations e.g. > pack unitcell 1555 2555 > or out of the unitcell > pack unitcell 1555 2456 Jan, I do not understand the notation that you are using. > http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_74.html I will read this > I think this would be in general a nice formating feature but I would > use %7.2x for 2 digits right, e.g. > label "%5i [%n]%r^%I:%c.%a;%A/%M\n%2e%C %8.3x %8.3y %8.3z %b" I think you are right ... more like printf >>What do you think about doing the same thing for atoms? When you hover >> over an atom for a while the 'hover' window would appear. >> >>Q: In general, would this be useful functionality? >> >> > Yes, onClick? I do not now what you mean by onClick. onClick has the 'picking' behavior that prints out to the console (or calls the JavaScript function). What do you want onClick to do? > If you would like to parse the > HETNAM > FORMUL > records, maybe people want to use > hover " %h" > label "[%n]%r %f" I will look at these records. Miguel ------------------------------------------------------- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps & Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
