Bugs item #989312, was opened at 2004-07-12 12:18 Message generated for change (Comment added) made by migueljmol You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=989312&group_id=23629
Category: None Group: None Status: Open Resolution: None Priority: 5 Submitted By: Miguel (migueljmol) Assigned to: Miguel (migueljmol) >Summary: 2D structural diagrams Initial Comment: PMR points out that it would be useful to support 2D fisher projections. This would allow us to show molecules in both 2D and 3D formats. Quality of 2D rendering is very important. MarvinSketch has a good listing of standard formatting styles for fisher projections (explicit carbons, explicit hydrogens, only hydrogens connected to non-carbons, etc) The only rotation would be around the z axis. This should probably support only the same mouse gesture as the 3D world. I assume that zoom & translate should work the same. CML will support 5D (2D + 3D) and 8D (2D + 3D + fractional) coordinates. It will be important to support a smooth association between the 2D and the 3D coordinates. It should be possible to construct applications where hiliting in one world also hilites in the other. ---------------------------------------------------------------------- >Comment By: Miguel (migueljmol) Date: 2004-07-14 10:55 Message: Logged In: YES user_id=1050060 ---------------------------- Original Message ---------------------------- Subject: Re: [Jmol-developers] [ jmol-Bugs-989312 ] 2D fisher projections From: "Peter Murray-Rust" <[EMAIL PROTECTED]> Date: Wed, July 14, 2004 10:31 To: [EMAIL PROTECTED] -------------------------------------------------------------------------- [snip] Hi, I would actually avoid the use of the word "projection" completely. They are best called "chemical structure diagrams". They are sometimes created by projecting the 3D structure onto its principal axes but this is not normally pretty and it a last resort. JCP does this if it has only 3D coords, but I would immediately use the clean function to get a "better" layout. These diagrams may contain many other features which are not projections including abbreviated functional groups, labelling, polymer bead supports (a ball), group multipliers (polymers) , Markush ligands, etc. . P. ---------------------------------------------------------------------- Comment By: Miguel (migueljmol) Date: 2004-07-14 09:50 Message: Logged In: YES user_id=1050060 ---------------------------- Original Message ---------------------------- Subject: Re: [Jmol-developers] [ jmol-Bugs-989312 ] 2D fisher projections From: "Miguel" <[EMAIL PROTECTED]> Date: Wed, July 14, 2004 9:49 To: [EMAIL PROTECTED] -------------------------------------------------------------------------- Peter wrote: >>Initial Comment: >>PMR points out that it would be useful to support 2D >>fisher projections. This would allow us to show >>molecules in both 2D and 3D formats. Quality of 2D >>rendering is very important. MarvinSketch has a good >>listing of standard formatting styles for fisher >>projections (explicit carbons, explicit hydrogens, only >>hydrogens connected to non-carbons, etc) > > I think you mean "2D structural diagrams". [Fischer (sic) projections are a > (hopefully obsolescent) way of representing certain subsets of chemistry such as sugars and amino acids]. Note that the preferred conventions are being developed at: > http://www.angelfire.com/sc3/iupacstructures/ > which are the result of considerable recent discussion moderated by Jonathan Brecher of CambridgeSoft. Yes, I now understand that these are 2D projections ... and that a Fischer projection is a special type which has special interpretations for horizontal/vertical bond alignment. (Using google ... Fischer seemed more popular than Fisher) Miguel ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2004-07-12 14:31 Message: Logged In: NO As a side note: I'm working on a JCP plugin for Jmol... want to finish this in the next four weeks (my holiday)... BTW, I'm also in the process of getting ADSL at home, and got rid of ISDN, but my analog modem does not work on Linux, so I'm not so responsive for the next few weeks... Egon ---------------------------------------------------------------------- Comment By: Miguel (migueljmol) Date: 2004-07-12 12:20 Message: Logged In: YES user_id=1050060 fisher -> fischer ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=989312&group_id=23629 ------------------------------------------------------- This SF.Net email sponsored by Black Hat Briefings & Training. Attend Black Hat Briefings & Training, Las Vegas July 24-29 - digital self defense, top technical experts, no vendor pitches, unmatched networking opportunities. Visit www.blackhat.com _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
