Pdb use ter records - Revision history

Cchem: 2 revisions

2019-01-07T03:14:12Z

2 revisions

Speleo3: style

2018-12-17T12:32:04Z

style

Speleo3 at 12:29, 17 December 2018

2018-12-17T12:29:16Z

Bell: 3 revisions

2015-10-19T01:04:52Z

3 revisions

OsvaldoMartin: add see also (Pdb_conect_nodup and Pdb_Conect_All) put the PyMOL api example under the title "PyMOL API"

2015-09-15T23:26:57Z

add see also (Pdb_conect_nodup and Pdb_Conect_All) put the PyMOL api example under the title "PyMOL API"

OsvaldoMartin: fix broken link to PDB page (ter format) and add this page to the settings page

2015-09-15T23:03:06Z

fix broken link to PDB page (ter format) and add this page to the settings page

Pyadmin: 1 revision

2014-03-28T02:16:22Z

1 revision

Hongbo zhu: /* Example */

2012-10-22T11:09:29Z

Example

Hongbo zhu: create page about parameter pdb_use_ter_records

2012-10-22T11:08:21Z

create page about parameter pdb_use_ter_records

New page

When a molecule (e.g. a protein molecule) is saved in pdb format by PyMOL, a line of [http://www.wwpdb.org/documentation/format33/sect9.html#TER TER] record is inserted wherever the residue id is not sequential. To suppress this feature, set <tt>pdb_use_ter_records</tt> value to 0 before saving protein molecules.

=Example=
<source lang="python">
get pdb_use_ter_records # return current value of pdb_use_ter_records
set pdb_use_ter_records, 0
</source>

@@ Line 8: / Line 8: @@
 * <= 1.5.0.4 feature broken for HETATM polymer residues (e.g. MSE)
-===Example===
+== Example ==
 <source lang="python">
 get pdb_use_ter_records  # return current value of pdb_use_ter_records
@@ Line 14: / Line 14: @@
 </source>
-===PYMOL API===
+== PyMOL API ==
 <source lang="python">
 cmd.set('pdb_use_ter_records', 0)
 </source>
-===SEE ALSO===
+== See Also ==
-[[Pdb_conect_nodup]], [[Pdb_Conect_All]]
 [[Category:Settings|Pdb_use_ter_records]]

← Older revision		Revision as of 12:29, 17 December 2018
Line 1:		Line 1:
	When a molecule (e.g. a protein molecule) is saved in pdb format by PyMOL, a line of [http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#TER TER] record is inserted wherever the residue id is not sequential. To suppress this feature, set <tt>pdb_use_ter_records</tt> value to 0 before saving protein molecules.		When a molecule (e.g. a protein molecule) is saved in pdb format by PyMOL, a line of [http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#TER TER] record is inserted wherever the residue id is not sequential. To suppress this feature, set <tt>pdb_use_ter_records</tt> value to 0 before saving protein molecules.
		+
		+	== Version History ==
		+
		+	* 2.3.0 new implementation, [https://github.com/schrodinger/pymol-testing/commit/82440d760b6b2b48b2cb1ca6c0bb5347870a4541 works correctly with gaps]
		+	* 1.8.4 feature removed
		+	* <= 1.8.2 feature broken for various use cases (e.g. gaps)
		+	* <= 1.5.0.4 feature broken for HETATM polymer residues (e.g. MSE)

	===Example===		===Example===

@@ Line 1: / Line 1: @@
 When a molecule (e.g. a protein molecule) is saved in pdb format by PyMOL, a line of [http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#TER TER] record is inserted wherever the residue id is not sequential. To suppress this feature, set <tt>pdb_use_ter_records</tt> value to 0 before saving protein molecules.
-=Example=
+===Example===
 <source lang="python">
 get pdb_use_ter_records  # return current value of pdb_use_ter_records
 set pdb_use_ter_records, 0
-import cmd
+===PYMOL API===
-cmd.set(name='pdb_use_ter_records', value=0) # same effect
+<source lang="python">
 </source>
 [[Category:Settings|Pdb_use_ter_records]]

@@ Line 1: / Line 1: @@
-When a molecule (e.g. a protein molecule) is saved in pdb format by PyMOL, a line of [http://www.wwpdb.org/documentation/format33/sect9.html#TER TER] record is inserted wherever the residue id is not sequential. To suppress this feature, set <tt>pdb_use_ter_records</tt> value to 0 before saving protein molecules.
+When a molecule (e.g. a protein molecule) is saved in pdb format by PyMOL, a line of [http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#TER TER] record is inserted wherever the residue id is not sequential. To suppress this feature, set <tt>pdb_use_ter_records</tt> value to 0 before saving protein molecules.
 =Example=
@@ Line 9: / Line 9: @@
 cmd.set(name='pdb_use_ter_records', value=0) # same effect
 </source>

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