Support for bond orders - Revision history

AngelHerraez at 16:08, 5 October 2020

2020-10-05T16:08:19Z

AngelHerraez at 16:06, 5 October 2020

2020-10-05T16:06:36Z

AngelHerraez: display style for multiple bonds

2016-07-11T14:56:46Z

display style for multiple bonds

AngelHerraez: /* Display style */

2016-07-11T13:47:17Z

‎Display style

AngelHerraez: display style for multiple bonds

2016-07-11T13:32:05Z

display style for multiple bonds

AngelHerraez: more details on CML bond order

2009-06-19T09:15:05Z

more details on CML bond order

AngelHerraez: CML bond orders

2009-06-18T23:26:54Z

CML bond orders

AngelHerraez: redirect links to new subpages

2009-04-25T17:29:43Z

redirect links to new subpages

AngelHerraez: bond type 8 in MOL format

2008-09-25T19:25:25Z

bond type 8 in MOL format

AngelHerraez at 12:25, 12 July 2008

2008-07-12T12:25:15Z

@@ Line 69: / Line 69: @@
 <table style="width:100%;">
 <tr>
-<td>default
+<td>default<br> (set multipleBondSpacing -1)
 </td>
 <td>set multipleBondSpacing -0.3
@@ Line 137: / Line 137: @@
 <td>Double sticks perpendicular<br> to the plane of the ring.
 </td>
-<td>Double sticks curved,<br> perpendicular
+<td>Double sticks curved, perpendicular<br> to the plane of the ring.
 </td>
 </tr>
 </table>

@@ Line 59: / Line 59: @@
 You may opt for double sticks that are in the plane of the atoms involved (particularly significant for bonds in rings), using a positive 'N' value in <code>set multipleBondSpacing N</code>
-The default thickness and spacing of the sticks may be changed using <code>set multipleBondSpacing N</code> and <code>set multipleBondSpacing N</code>
+The default thickness and spacing of the sticks may be changed using <code>set multipleBondRadiusFactor N</code> and <code>set multipleBondSpacing N</code>
 There is also an alternative style using curved sticks, available with <code>set multipleBondBananas on</code>
 [{{ScriptingDoc}}#k875 Detailed documentation] for all these.
 <table style="width:100%;">
@@ Line 69: / Line 71: @@
 <td>default
 </td>
-<td>set multipleBondSpacing -0.5
+<td>set multipleBondSpacing -0.3
 </td>
-<td>set multipleBondSpacing 0.5
+<td>set multipleBondSpacing 0.4
 </td>
 <td>set multipleBondBananas on
@@ Line 80: / Line 84: @@
 <jmol>
    <jmolApplet>
-     <size>200</size>
+     <size>240</size>
      <urlContents>https://cactus.nci.nih.gov/chemical/structure/caffeine/sdf</urlContents>
-     <script>initialize;spin on;</script>
+     <script>initialize;set multipleBondSpacing 0.4;</script>
    </jmolApplet>
 </jmol>
@@ Line 89: / Line 111: @@
 <jmol>
    <jmolApplet>
-     <size>200</size>
+     <size>240</size>
      <urlContents>https://cactus.nci.nih.gov/chemical/structure/caffeine/sdf</urlContents>
-     <script>initialize;set multipleBondSpacing -0.5;spin on;</script>
+     <script>initialize;set multipleBondSpacing 0.3; set multipleBondRadiusFactor -1;</script>
    </jmolApplet>
 </jmol>
@@ Line 98: / Line 120: @@
 <jmol>
    <jmolApplet>
-     <size>200</size>
+     <size>240</size>
      <urlContents>https://cactus.nci.nih.gov/chemical/structure/caffeine/sdf</urlContents>
-     <script>initialize;set multipleBondSpacing 0.5;spin on;</script>
+     <script>initialize;set multipleBondBananas on;</script>
    </jmolApplet>
 </jmol>
 </td>
 <td>
-[[file:Caffeine_rotating_bananas_200px.gif]]
+Always seen as double sticks,<br> facing the viewer.
 </td>
 </tr>
 </table>

@@ Line 82: / Line 82: @@
      <size>200</size>
      <urlContents>https://cactus.nci.nih.gov/chemical/structure/caffeine/sdf</urlContents>
-     <script>initialize</script>
+     <script>initialize;spin on;</script>
    </jmolApplet>
 </jmol>
@@ Line 91: / Line 91: @@
      <size>200</size>
      <urlContents>https://cactus.nci.nih.gov/chemical/structure/caffeine/sdf</urlContents>
-     <script>initialize;set multipleBondSpacing -0.5;</script>
+     <script>initialize;set multipleBondSpacing -0.5;spin on;</script>
    </jmolApplet>
 </jmol>
@@ Line 100: / Line 100: @@
      <size>200</size>
      <urlContents>https://cactus.nci.nih.gov/chemical/structure/caffeine/sdf</urlContents>
-     <script>initialize;set multipleBondSpacing 0.5;</script>
+     <script>initialize;set multipleBondSpacing 0.5;spin on;</script>
    </jmolApplet>
 </jmol>
 </td>
 <td>
-<jmol>
+[[file:Caffeine_rotating_bananas_200px.gif]]
 </td>
 </tr>
 </table>

@@ Line 57: / Line 57: @@
 By default, Jmol displays double bonds as twin sticks (cylinders) contained in the viewer's plane, i.e. always visible as double sticks.
-You may opt for double sticks that are in the plane of the atoms involved (particularly significant for bonds in rings), using a negative 'N' value in <code>set multipleBondRadiusFactor N</code>
+You may opt for double sticks that are in the plane of the atoms involved (particularly significant for bonds in rings), using a positive 'N' value in <code>set multipleBondSpacing N</code>
 The default thickness and spacing of the sticks may be changed using <code>set multipleBondSpacing N</code> and <code>set multipleBondSpacing N</code>
@@ Line 64: / Line 64: @@
 [{{ScriptingDoc}}#k875 Detailed documentation] for all these.

@@ Line 3: / Line 3: @@
 Visualization of non-single bonds can be supressed (all will show as single) if
 <code>[http://chemapps.stolaf.edu/jmol/docs/#setbondstyles set showMultipleBonds off]</code> is issued at the console or from a script.
 File formats that specify bond order --and Jmol recognizes as such:
@@ Line 51: / Line 53: @@
 (f) not fully implemented; starting Jmol 11.7.32 only partial12 is implemented

@@ Line 8: / Line 8: @@
 * [[File_formats/Coordinates#MOL2_.28Sybyl.2C_Tripos.29|MOL2]] specifies bond order natively, using certain alphanumeric codes (see table below)
 * [[File_formats/Coordinates#PDB|PDB]] can do double bonds using a trick: specify '''twice''' each [http://www.wwpdb.org/documentation/format23/sect10.html CONECT record], or put the second atom twice in the same record.
-* CML specifies 'partial12' bond order, which is implemented by Jmol starting 11.7.32
+* CML specifies bond order natively, using XML tags; Jmol implements single, double, triple, aromatic and 'partial12'.
 Jmol commands that assign bond order:
@@ Line 21: / Line 21: @@
 |  || hBond <sup>a</sup> || -1 || n/a || n/a || hbond
 |-align="center"
-| 0.5 || partial <sup>a</sup> || 0.5 || 8 <sup>d</sup> || n/a || partial01
+| 0.5 || partial <sup>a</sup> || 0.5 || 8 <sup>d</sup> || n/a || partial01 <sup>f</sup>
 |-align="center"
 | 1 || single || 1 || 1 || 1 || 1 or S
@@ Line 31: / Line 31: @@
 | 2 || double || 2 || 2 || 2 || 2 or D
 |-align="center"
-| 2.5 || partialTriple ? <sup>c</sup> || 2.5 or -2.5 <sup>b,c</sup> || n/a || n/a || partial23
+| 2.5 || partialTriple ? <sup>c</sup> || 2.5 or -2.5 <sup>b,c</sup> || n/a || n/a || partial23 <sup>f</sup>
 |-align="center"
 | 3 || triple || 3 || 3 || 3 || 3 or T
@@ Line 50: / Line 50: @@
 (e) as documented at http://eugen.leitl.org/nesc/jumbo4.3/schemas/cmlAll/htmldocs/orderType.html
-(f) starting Jmol 11.7.32
+(f) not fully implemented; starting Jmol 11.7.32 only partial12 is implemented

@@ Line 5: / Line 5: @@
 File formats that specify bond order --and Jmol recognizes as such:
-* [[File_formats#.28MDL.29_MOL_and_SD|MOL]] specifies bond order natively, using certain numeric codes (see table below)
+* [[File_formats/Coordinates#MOL_and_SD_.28Symyx_MDL.29|MOL]] specifies bond order natively, using certain numeric codes (see table below)
-* [[File_formats#.28Sybyl.29_MOL2|MOL2]] specifies bond order natively, using certain alphanumeric codes (see table below)
+* [[File_formats/Coordinates#MOL2_.28Sybyl.2C_Tripos.29|MOL2]] specifies bond order natively, using certain alphanumeric codes (see table below)
-* [[File_formats#PDB|PDB]] can do double bonds using a trick: specify '''twice''' each [http://www.wwpdb.org/documentation/format23/sect10.html CONECT record].
+* [[File_formats/Coordinates#PDB|PDB]] can do double bonds using a trick: specify '''twice''' each [http://www.wwpdb.org/documentation/format23/sect10.html CONECT record], or put the second atom twice in the same record.
 Jmol commands that assign bond order:

@@ Line 20: / Line 20: @@
 |  || hBond <sup>a</sup> || -1 || n/a || n/a
 |-align="center"
-| 0.5 || partial <sup>a</sup> || 0.5 || 8 ? <sup>d</sup> || n/a
+| 0.5 || partial <sup>a</sup> || 0.5 || 8 <sup>d</sup> || n/a
 |-align="center"
 | 1 || single || 1 || 1 || 1
@@ Line 45: / Line 45: @@
 (c) starting Jmol 11.3.28
-(d) type 8 is defined as "any" in MOL format; rendering varies across Jmol versions (none, partial, partially double)
+(d) type 8 is defined as "any" in MOL format; most versions of Jmol will render that as partial.