Bugs item #899782, was opened at 2004-02-18 13:27 Message generated for change (Settings changed) made by migueljmol You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=899782&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 Resolution: None Priority: 5 Submitted By: Miguel (michaelthoward) Assigned to: Miguel (migueljmol) Summary: add radical support Initial Comment: John said: > A simple example: > The allyl radical is formally H2C=CH-CH2 and is normally written with > a bullet > superscript on the rightmost carbon atom C to indicate the presence of > an unpaired electron on that carbon. Understood > If the hydrogen atoms are not displayed then the presence of the bullet > is essential > as otherwise C=C-C could represent H2C=CH-CH3 That makes sense > The following is my version of a mol file with the 'radical' information > added but because it doesn't work I don't know if I have followed the > MOL format specs. > correctly. The M RAD line is saying (?) there is one atom, namely atom > no. 2 which has an unpaired electron [snip] > M RAD 1 2 2 Q: What is that 'extra' 2 ? OK. The bad news is that these RAD records are not being read by Jmol. Even worse is that there is no support for anything like this ... since this is the first that I have heard of it :-) The good news is that I don't think it would be too difficult to add. Q: Is it enough to say that it is a 'radical', or is there some measure of 'radicalness'? :-) Basically, can I just use one bit as a flag to tell whether or not something is 'radical'? Q: What is the relationship (if any) between 'radical' and 'charge'? You earlier asked about showing the atom 'name'. I think this would be a good case to give this atom a different 'name': if you say label "%e" you will get 'C' if you say label "%a" you will get 'C*' [bullet] Q: does that sound right to you? Separately, did label "%C" work for you? Miguel -------- Original Message -------- Subject: Re: [Jmol-users] JMol applet: label option From: John Simmie <[EMAIL PROTECTED]> Date: Wed, February 18, 2004 18:27 To: [email protected] Miguel: A simple example: The allyl radical is formally H2C=CH-CH2 and is normally written with a bullet superscript on the rightmost carbon atom C to indicate the presence of an unpaired electron on that carbon. If the hydrogen atoms are not displayed then the presence of the bullet is essential as otherwise C=C-C could represent H2C=CH-CH3 The following is my version of a mol file with the 'radical' information added but because it doesn't work I don't know if I have followed the MOL format specs. correctly. The M RAD line is saying (?) there is one atom, namely atom no. 2 which has an unpaired electron ----------------------------------------------------------------------------------- HCOO_opt created with ArgusLab version 4.0.0 Beta Release #2 4 3 0 0 0 0 0 0 0 0 0 V2000 -0.4525 0.1224 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0961 1.1697 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0725 -1.0434 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6576 0.0125 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1 3 2 0 0 0 0 1 2 1 0 0 0 0 1 4 1 0 0 0 0 M RAD 1 2 2 M END ----------------------------------------------------------------------------------- All the best, John ---------------------------------------------------------------------- Comment By: Miguel (michaelthoward) Date: 2004-02-19 04:43 Message: Logged In: YES user_id=608250 At 17:52 18/02/2004, you wrote: >John said: > > correctly. The M RAD line is saying (?) there is one atom, namely atom > > no. 2 which has an unpaired electron >[snip] > > M RAD 1 2 2 >Q: What is that 'extra' 2 ? An atom can have no unpaired electrons, 1 unpaired e, or 2 unpaired es but the coding used by the mol file is 1, 2 or 3 (singlet, doublet or triplet electronic states) So the second 2 means that carbon has one unpaired electron. >Q: Is it enough to say that it is a 'radical', or is there some measure of >'radicalness'? :-) Basically, can I just use one bit as a flag to tell >whether or not something is 'radical'? > >Q: What is the relationship (if any) between 'radical' and 'charge'? The short answer is none; note that the mol file treats them separately M CHG 2 4 1 6 -1 means that two atoms have charges with atom no. 4 having a formal positive charge whilst atom no. 6 has a formal -ve charge >You earlier asked about showing the atom 'name'. I think this would be a >good case to give this atom a different 'name': > if you say label "%e" you will get 'C' > if you say label "%a" you will get 'C*' [bullet] > >Q: does that sound right to you? Yes I think so; this is basically a labelling issue. >Separately, did label "%C" work for you? >Miguel Dr. John M. Simmie Chemistry Department & Environmental Change Institute National University of Ireland, Galway::Ireland Phone: +353-91-750388::Fax: +353-91-525700 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=899782&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
