Feature Requests item #964835, was opened at 2004-06-02 03:26 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=964835&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Priority: 5 Submitted By: Miguel (migueljmol) Assigned to: Bob Hanson (hansonr) Summary: deal with lone pairs Initial Comment: need to come up with some strategy/approach for dealing with lone pairs of electrons ... as in samples/xyz/met-enkaphalin_movie.xyz ---------------------------- Original Message ---------------------------- Subject: Re: [Jmol-developers] element symbol LP From: "Bob Hanson" <[EMAIL PROTECTED]> Date: Tue, June 1, 2004 18:52 To: [email protected] -------------------------------------------------------------------------- Rendering of a lone pair would be nice. I suppose someone out there has a program that wants to "fake" a display of a lone pair of electrons. This could take the shape of anything from a teardrop (point on closest atom; center of tear on xyz coordinate) or, more likely, just a pair of dots like this: X : whose imaginary connecting line is perpendicular to the line connecting the xyz coordinate to that of the nearest atom. Chime ignores these. Miguel wrote: >>>The file samples/xyz/met-enkaphalin_movie.xyz contains the element symbol >>>'LP' >>>... >>>H 2.056 2.462 -4.930 >>>S 3.057 4.570 -4.353 >>>LP 3.502 4.170 -4.030 >>>LP 2.652 5.106 -4.475 >>>C 3.658 4.243 -6.025 >>>H 4.409 3.452 -5.958 >>>... >>> >>>Do you know what this is supposed to be? >> >>Lone pair. ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2006-03-06 23:16 Message: Logged In: YES user_id=1082841 lone pairs are displayed as single pink balls unconnected to any element. To connect: connect 1.2 (all) (all) would do it. But it will still be a single ball instead of twins. Not ideal, but it will have to do. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2004-07-15 09:13 Message: Logged In: YES user_id=1082841 Miguel, Rendering: Yes, there should be a VERY close atom. In the case sited, it's 68 pm--a very short distance. Shouldn't be any problem at all. I think it's important to identify that atom and to place the two dots on a perpendicular to the line connecting the "LP" and atom X. Default Color: white I would stay far away from the "tear-drop" idea. While some lone pairs have that nature, many do not. (Some are more p-orbital shaped, for example, and some are spherical.) Applying that model to all seems inappropriate to me. Of course, I suppose if someone has PLACED the LP in the file, maybe they do want them rendered as tear drops. Hmm. Later on that. Bob ---------------------------------------------------------------------- Comment By: Miguel (migueljmol) Date: 2004-07-15 04:50 Message: Logged In: YES user_id=1050060 Bob, Within Jmol we will represent a Lone Pair as an atom with some high element number (110 or something like that). Internally, its element symbol will be Lp. The 'p' needs to be lower case because all elements have a lower case second letter. We probably will be able to render it as ALLCAPS LP for display purposes. The easiest way to render a lone pair would be as two small spheres. The Lp *atom* would have a size just like all atoms. But we would scale this size by a factor of 8 (or something). The simplest thing would be to always display the Lp in the vertical vertical orientation or horizontal if you prefer). That way, we don't have to make the rendering a function of the orientation. If we *do* want to change the orientation of the Lp during rendering, then we need to associate the Lp with an atom. This means making a bond in the internal data structures between the Lp and its associated atom. If we did this, then we could orient the dots so that they were always perpedicular to their associated atom. But, this means that we need to have some way to identify which atom the Lp is bonded to. The only place I have ever seen an Lp is in a .xyz file ... where there is no connectivity information. Q: How does one determine which atom an Lp is associated with? Is it the closest one. Q: By default, what color should an Lp be? After we do all of this, then we can think about changing the shape to a teardrop (or whatever). ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=964835&group_id=23629 ------------------------------------------------------- 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
