Bugs item #933235, was opened at 2004-04-11 17:04 Message generated for change (Settings changed) made by migueljmol You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=933235&group_id=23629
Category: File Input/Output Group: None Status: Closed Resolution: Fixed Priority: 5 Submitted By: Miguel (michaelthoward) >Assigned to: Miguel (migueljmol) Summary: cif connectivity Initial Comment: ---------------------------- Original Message ---------------------------- Subject: CIF connectivity From: "Miguel" <[EMAIL PROTECTED]> Date: Sun, April 11, 2004 16:55 To: [EMAIL PROTECTED] -------------------------------------------------------------------------- >> > But I'm not certain what a *rendering program* is supposed to _do_ with the bond lengths, >> One good use for Jmol to parse the bond-length data (assuming it is present) >> is to define the connectivity for those "bonds" that may not be automaticallyfound by the program. > > I see your point (I'm thinking 'aloud' for Miguel's benefit too, since he > posed the question): Connectivity could be established w/o considering the > bond lengths themselves: [Ga1 O2 x.xx(x)] for example would fill the connectivity with bonds btwn any of the Ga1 and O2 positions, but x.xxA condition would limit those bonds to near atoms. I will plan on extending the CIF reader to use the _geom_bond_* data to determine connectivity. At this time the bond distance data will not be used. There has been a separate request to store arbitrary properties associated with a bond. At the present time that is not easy to do because there is currently no concept of bonds having properties and/or labels ... only atoms have properties/labels. If/when that gets implemented then we can consider storing the bond distance + bond error as a bond property. Q: What are other properties that may be of interest when looking at a bond? Q: What does esd stand for? Miguel ---------------------------------------------------------------------- Comment By: Miguel (michaelthoward) Date: 2004-05-14 20:34 Message: Logged In: YES user_id=608250 Done. Bond distances are read within .cif files in order to build the bond connectivity table. The bond distances themselves are not currently used. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=933235&group_id=23629 ------------------------------------------------------- This SF.Net email is sponsored by: Oracle 10g Get certified on the hottest thing ever to hit the market... Oracle 10g. Take an Oracle 10g class now, and we'll give you the exam FREE. http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
