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Hongbo zhu (talk | contribs) (new page about setting pdb_conect_nodup and tricks to store bond order in PDB files.) |
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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]. | 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=on</tt>) and the setting allows you to switch that off (<tt>pdb_conect_nodup=on</tt>). <ref></ref> |
| − | |||
== Syntax == | == Syntax == | ||
<source lang="python"> | <source lang="python"> | ||
| + | get pdb_conect_nodup # get current value | ||
set pdb_conect_nodup, 1 # no CONECT duplication is used to store bond order | set pdb_conect_nodup, 1 # no CONECT duplication is used to store bond order | ||
</source> | </source> | ||
| + | == Notes == | ||
| + | [http://sourceforge.net/p/pymol/mailman/message/32735483/ PyMOL user mailing list discussion on <tt>pdb_conect_nodup</tt>] | ||
[[Category:Settings|pdb_conect_nodup]] | [[Category:Settings|pdb_conect_nodup]] | ||
Revision as of 08:26, 20 August 2014
Overview
The pdb_conect_nodup setting in pymol controls if duplicated connectivity record (CONECT) in saved PDB is used to stored 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 (pdb_conect_nodup=on) and the setting allows you to switch that off (pdb_conect_nodup=on). Cite error: Invalid <ref> tag; refs with no name must have content
Syntax
get pdb_conect_nodup # get current value
set pdb_conect_nodup, 1 # no CONECT duplication is used to store bond order