Pdb conect all - Revision history

Bell: 5 revisions

2015-11-16T05:01:09Z

5 revisions

Speleo3 at 19:30, 9 November 2015

2015-11-09T19:30:48Z

Speleo3: moved Pdb Conect All to Pdb conect all: capitals

2015-11-09T18:59:58Z

moved Pdb Conect All to Pdb conect all: capitals

OsvaldoMartin: add see also (Pdb_conect_nodup and Pdb_use_ter_recordsl)

2015-09-15T23:29:47Z

add see also (Pdb_conect_nodup and Pdb_use_ter_recordsl)

OsvaldoMartin at 17:13, 14 September 2015

2015-09-14T17:13:12Z

New page

== Introduction ==
'''pdb_conect_all''' turns on/off the ability of PyMol to save the '''CONECT''' data in a PDB file.

=== Values ===
*off turns the feature off
*on turns the feature on

=== Example ===
<source lang="python">
set pdb_conect_all, on
</source>

=== PyMOL API ===
<source lang="python">
cmd.set('pdb_conect_all', 'on')
</source>

[[Category:Settings|Pdb_conect_all]]

← Older revision	Revision as of 05:01, 16 November 2015
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-== Introduction ==
+When saving a PDB file, the [[pdb_conect_all]] settings controls whether PyMOL writes CONECT records for all bonds, or only for HETATM bonds.
-=== Values ===
+PDB files by convention do not contain bond information for standard polymer residues (ATOM records), because the connectivity is known for those.
 *off turns the feature off
-*on turns the feature on
+If a PDB file contains at least one CONECT record for two atoms from ATOM records, then PyMOL will set '''pdb_conect_all=on''' as an object-level setting, to again write CONECT records for all bonds when saving that object to a PDB file.
 <source lang="python">
 set pdb_conect_all, on
 </source>
-=== PyMOL API ===
+Now the file '''1rx1_conect_all.pdb''' contains 1316 CONECT records.
-<source lang="python">
-cmd.set('pdb_conect_all', 'on')
+== See Also ==
-=== See Also ===
+* [[connect_mode]]
-[[Pdb_conect_nodup]], [[Pdb_use_ter_records]]
+* [[pdb_ignore_conect]]
 [[Category:Settings|Pdb_conect_all]]

← Older revision	Revision as of 18:59, 9 November 2015
(No difference)