Support for stereochemistry - Revision history

AngelHerraez at 08:52, 21 May 2010

2010-05-21T08:52:47Z

AngelHerraez: adding links

2010-04-30T21:58:41Z

adding links

AngelHerraez: stereo bonds

2010-04-30T21:54:34Z

stereo bonds

AngelHerraez: /* MOL formats */

2010-04-30T19:37:35Z

‎MOL formats

AngelHerraez: new section for stereochemistry support

2010-04-30T18:56:16Z

new section for stereochemistry support

New page

Jmol supports stereochemistry in some 2D file formats.

== MOL formats ==
''This includes all formats based on the chemical table files (CTfiles) specification from MDL/Symyx, like <code>mol</code>, <code>sdf</code>, etc.''

In the CTfile specification, stereochemistry is specified in the bond line, columns 10-12, with a numeric code (see the table).
If the model is flat (2D, all atoms have Z=0) '''and''' the <code>filter "2D"</code> switch is used in the <code>load</code> command, Jmol v.12 will use the stereo information to build a 3D model.

== JME format ==
This is only a 2D format, but allows specification of "up" and "down" wedge bonds (see the table).
Jmol v.12 reads these and uses them when converting the model to 3D, which is done automatically upon load.

== Bond codes ==
{| border="1" cellpadding="5" cellspacing="0"
|-align="center"
! stereo bond !! bond code in MOL file !! bond code in JME file
|-align="center"
| up || 1 || -1
|-align="center"
| down || 6 || -2
|}

@@ Line 6: / Line 6: @@
 In the CTfile specification, stereochemistry is specified in the bond line, columns 10-12 (the 4th number in the row), with a numeric code (see the table).
-If the model is flat (2D, all atoms have Z=0) '''and''' the <code>filter "2D"</code> switch is used in the <code>load</code> command, Jmol v.12 will use the stereo information to build a 3D model. After that, the bonds will be assigned as single.
+If the model is flat (2D, all atoms have Z=0) '''''and''''' the <code>filter "2D"</code> switch is used in the <code>load</code> command, Jmol v.12 will use the stereo information to build a 3D model. After that, the bonds will be assigned as single.
 == JME format ==

@@ Line 2: / Line 2: @@
 == MOL formats ==
-''This includes all formats based on the chemical table files (CTfiles) specification from MDL/Symyx, like <code>mol</code>, <code>sdf</code>, etc.''
+''This includes all formats based on the chemical table files (CTfiles) specification from MDL/Symyx, like
 In the CTfile specification, stereochemistry is specified in the bond line, columns 10-12 (the 4th number in the row), with a numeric code (see the table).
@@ Line 8: / Line 9: @@
 == JME format ==
-This is only a 2D format, but allows specification of "up" and "down" wedge  bonds (see the table).
+This ([[File_formats/Coordinates#JME|Peter Ertl's JME Molecular Editor]]) is only a 2D format, but allows specification of "up" and "down" wedge  bonds (see the table).
 Jmol v.12 reads these and uses them when converting the model to 3D, which is done automatically upon load. After that, the bonds will be assigned as single.