Pdb conect nodup - Revision history

Bell: 3 revisions

2015-10-19T01:04:52Z

3 revisions

2015-09-15T23:31:03Z

2015-09-15T23:30:01Z

add see also (Pdb_conect_all and Pdb_use_ter_recordsl)

2015-09-15T23:00:05Z

fix broken link to PDB page (conect format)

2014-09-16T03:22:05Z

6 revisions

2014-08-20T09:40:00Z

Notes: add spcification of aromatic bonds

2014-08-20T08:29:14Z

Notes: add link to jmol support for bond order

2014-08-20T08:27:24Z

Overview

2014-08-20T08:26:43Z

Overview

2014-08-20T08:26:29Z

@@ Line 16: / Line 16: @@
 === See Also ===
-[[Pdb_conect_all]], [[Pdb_use_ter_records]]
+[[Pdb_Conect_All]], [[Pdb_use_ter_records]]
 [[Category:Settings|pdb_conect_nodup]]

@@ Line 14: / Line 14: @@
 * Jmol support for bond order: http://wiki.jmol.org/index.php/Support_for_bond_orders
 * Aromatic bonds are stored using four duplication of the same CONECT records, as specified in, for example, MOL format. See http://wiki.jmol.org/index.php/Support_for_bond_orders
 [[Category:Settings|pdb_conect_nodup]]

@@ Line 1: / Line 1: @@
 == Overview ==
-The '''pdb_conect_nodup''' setting in pymol controls if duplicated connectivity record ([http://www.wwpdb.org/documentation/format23/sect10.html CONECT]) in saved PDB is used to stored [http://en.wikipedia.org/wiki/Bond_order bond order].
+The '''pdb_conect_nodup''' setting in pymol controls if duplicated connectivity record ([http://www.wwpdb.org/documentation/file-format-content/format33/sect10.html#CONECT CONECT]) in saved PDB is used to stored [http://en.wikipedia.org/wiki/Bond_order bond order].
 This is an unofficial PDB feature to store bond order and is supported by several applications that read PDB files, but may break PDB file loading in other applications which don't support it. PyMOL always wrote duplicated connect records (<tt>pdb_conect_nodup=0</tt>) and the setting allows you to switch that off (<tt>pdb_conect_nodup=1</tt>).

@@ Line 13: / Line 13: @@
 * PyMOL user mailing list discussion on <tt>pdb_conect_nodup</tt>: http://sourceforge.net/p/pymol/mailman/message/32735483/
 * Jmol support for bond order: http://wiki.jmol.org/index.php/Support_for_bond_orders
+* Aromatic bonds are stored using four duplication of the same CONECT records, as specified in, for example, MOL format. See http://wiki.jmol.org/index.php/Support_for_bond_orders
 [[Category:Settings|pdb_conect_nodup]]

@@ Line 11: / Line 11: @@
 == Notes ==
-[http://sourceforge.net/p/pymol/mailman/message/32735483/ PyMOL user mailing list discussion on <tt>pdb_conect_nodup</tt>]
+* PyMOL user mailing list discussion on <tt>pdb_conect_nodup</tt>: http://sourceforge.net/p/pymol/mailman/message/32735483/
 [[Category:Settings|pdb_conect_nodup]]

← Older revision	Revision as of 01:04, 19 October 2015
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← Older revision	Revision as of 03:22, 16 September 2014
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 The '''pdb_conect_nodup''' setting in pymol controls if duplicated connectivity record ([http://www.wwpdb.org/documentation/format23/sect10.html CONECT]) in saved PDB is used to stored [http://en.wikipedia.org/wiki/Bond_order bond order].
-This is an unofficial PDB feature to store bond order and is supported by several applications that read PDB files, but may break PDB file loading in other applications which don't support it. PyMOL always wrote duplicated connect records (<tt>pdb_conect_nodup=on</tt>) and the setting allows you to switch that off (<tt>pdb_conect_nodup=on</tt>).
+This is an unofficial PDB feature to store bond order and is supported by several applications that read PDB files, but may break PDB file loading in other applications which don't support it. PyMOL always wrote duplicated connect records (<tt>pdb_conect_nodup=0</tt>) and the setting allows you to switch that off (<tt>pdb_conect_nodup=1</tt>).
 == Syntax ==

@@ Line 2: / Line 2: @@
 The '''pdb_conect_nodup''' setting in pymol controls if duplicated connectivity record ([http://www.wwpdb.org/documentation/format23/sect10.html CONECT]) in saved PDB is used to stored [http://en.wikipedia.org/wiki/Bond_order bond order].
-This is an unofficial PDB feature to store bond order and is supported by several applications that read PDB files, but may break PDB file loading in other applications which don't support it. PyMOL always wrote duplicated connect records (<tt>pdb_conect_nodup=on</tt>) and the setting allows you to switch that off (<tt>pdb_conect_nodup=on</tt>){{cite mailing list |title=PyMOL user mailing list discussion |url=http://sourceforge.net/p/pymol/mailman/message/32735483/}}.
+This is an unofficial PDB feature to store bond order and is supported by several applications that read PDB files, but may break PDB file loading in other applications which don't support it. PyMOL always wrote duplicated connect records (<tt>pdb_conect_nodup=on</tt>) and the setting allows you to switch that off (<tt>pdb_conect_nodup=on</tt>). <ref></ref>
 == Syntax ==
 <source lang="python">
 set pdb_conect_nodup, 1  # no CONECT duplication is used to store bond order
 </source>
 [[Category:Settings|pdb_conect_nodup]]