Bob Hanson wrote:
> The issue at hand has less to do with what is actually visible than
> what ATOMS are identified as being visible. I'd like to know what YOU
> would expect from commands such as:
>
> select visible
> center visible
> getProperty("atomInfo","visible")
>
> Specifically:
>
> Q: In a protein or nucleic acid model, where one might display trace,
> backbone, cartoon, ribbons, rockets, etc., independently of the atoms
> or bonds themselves, what would YOU say should constitute "visible"
> when only one of these renderings is in front of you?I think this might depend on the level someone is working at. Since I am mainly working at the residue/group level, I would expect that all atoms belonging to a group would be flagged as visible, independent of the rendering types that are currently activated for this group. It must of course be activated at least one rendering type. But this might be different for someone who works at the atom level. > > For example, for a protein: > > Q: If only the "backbone", which connects alpha-carbons is visible, > then should only those alpha carbons be identified as "visible"? > > Q: If only a "trace" is visible, which does not go exactly through any > particular atoms, then should any atoms be identified as "visible"? > > Q: What if we defined "visible" as "the atom is visible as a ball, > stick, star, halo, or dots, or the residue containing that atom is > visible in some Rasmol form"? Would that be logical? natural? too > strange? Maybe it should be distinguished between 'visible' and 'rendered'. (This reminds me of a related issue: currently 'restrict' eliminates all rendering information so that you cannot just hide something and later switch it on again with the same rendering. Maybe the visibility flag could also be used to build a 'hide' command, which would be very useful.) Regards, Rolf ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
