Fetch - Revision history

Cchem: 1 revision

2019-03-04T03:58:19Z

1 revision

Speleo3: PyMOL 2.3 quiet=0

2019-02-11T08:28:37Z

PyMOL 2.3 quiet=0

Cchem: 1 revision

2017-04-03T02:46:00Z

1 revision

Speleo3: version changes

2017-03-09T18:04:03Z

version changes

Pyadmin: 24 revisions

2014-03-28T02:00:41Z

24 revisions

Speleo3: proxy

2013-04-17T08:43:03Z

proxy

Tlinnet: /* Example 3 - multistate */

2013-03-01T17:24:00Z

Example 3 - multistate

Tlinnet: /* Example 3 */

2013-03-01T17:23:52Z

Example 3

Tlinnet: /* Syntax */

2013-03-01T17:21:51Z

Syntax

Hongbo zhu: /* Example */ add example of multiple commands in one line

2012-10-19T13:25:32Z

Example: add example of multiple commands in one line

@@ Line 5: / Line 5: @@
 == ChangeLog ==
 ''New in PyMOL 1.8.6: Support type=mmtf and [[fetch_type_default]] setting''
@@ Line 31: / Line 33: @@
 * '''name''' = str: new object name {default: accession code}
 * '''type''' = cif|mmtf|pdb|pdb1|2fofc|fofc|emd|cid|sid|cc: file type and/or accession code type {default: negotiated by code or use [[fetch_type_default]]}
-* '''async''' = 0/1: Download structures in the background and do not block the PyMOL command line. '''For scripting, you typically need async=0.''' {default: !quiet, which means 0 for the PyMOL command language, and 1 for the Python API}
+* '''async''' = 0/1: Download structures in the background and do not block the PyMOL command line. '''For scripting, you typically need async=0.''' {default: 0 since PyMOL 2.3, before that: !quiet, which means 1 for the PyMOL command language, and 0 for the Python API}
 ''Other arguments: See [[load]] command.''

@@ Line 1: / Line 1: @@
-'''Fetch''' retrieves a protein structure from the PDB and loads it into PyMOL.  The PDB file is saved in the current working directory for PyMOL.
+'''Fetch''' retrieves a protein structure from the PDB and loads it into PyMOL.
-You can now fetch electron density maps using ''type=fofc'' or ''type=2fofc''.  The map will be loaded if the electron density map exists on the [http://eds.bmc.uu.se/eds/ EDS] server.
+To download a so-called [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies biological assembly or biological unit], use the [[assembly]] setting or use ''type=pdb1'', ''type=pdb2'' and so on.
-=== Syntax ===
+== ChangeLog ==
-<source lang="python">
-fetch PDB_ID [ ID2 ... IDN ] [,type=[fofc,2fofc,pdb1]] [,multiplex= [0,1]] [,async = [0,1]]
+''New in PyMOL 1.8.6: Support type=mmtf and [[fetch_type_default]] setting''
-</source>
-To specify more than one PDB, just add its ID to the command line (separated by spaces).
+''Other arguments: See [[load]] command.''
-=== Proxy Setting ===
+== Proxy Setting ==
 If your network requires a proxy server, you can specify it by 'http_proxy' and 'ftp_proxy' environmental variables. At least in Mac OS X, these values are setup automatically. Otherwise, add to your [[pymolrc]] script:
@@ Line 20: / Line 44: @@
 os.environ["ftp_proxy"] = os.environ["http_proxy"]
 </syntaxhighlight>
 === Example ===
@@ Line 75: / Line 101: @@
 </source>
-= See Also =
+== See Also ==
-[[Fetch_Path]], [[Fetch_Host]], [[FetchLocal]]
 [[Category:Commands|Fetch]]

@@ Line 13: / Line 13: @@
 === Proxy Setting ===
-If your network requires a proxy server, you can specify it by 'http_proxy' and 'ftp_proxy' environmental variables.
+If your network requires a proxy server, you can specify it by 'http_proxy' and 'ftp_proxy' environmental variables. At least in Mac OS X, these values are setup automatically. Otherwise, add to your [[pymolrc]] script:
-At least in Mac OS X, these values are setup automatically. Otherwise, add
+<syntaxhighlight lang="python">
+import os
- <nowiki>export http_proxy='http://proxy.server.name:port/'</nowiki>
+os.environ["http_proxy"] = "http://username:password@proxy.server.name:port/"
- <nowiki>export ftp_proxy='http://proxy.server.name:port/' # shouldn't start with ftp://...</nowiki>
+os.environ["ftp_proxy"] = os.environ["http_proxy"]
+</syntaxhighlight>
 === Example ===

@@ Line 69: / Line 69: @@
 </source>
-=== Example 3 - multistate===
+=== Example 4 - multistate===
 This will fetch the biological assembly (type=pdb1) from the pdb, split the 60 states into separate objects (multiplex=1), and tell PyMOL to wait for all this to be completed before moving to the next command in a .pml script (async=0).
 <source lang="python">

@@ Line 60: / Line 60: @@
 </source>
-=== Example 3 ===
+=== Example 3 - pdb1===
 <source lang="python">
 # fetch the biological assembly of 1avd
@@ Line 67: / Line 67: @@
 fetch 1avd, type=pdb1
 split_state 1avd
 </source>

← Older revision	Revision as of 03:58, 4 March 2019
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← Older revision	Revision as of 02:46, 3 April 2017
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← Older revision	Revision as of 02:00, 28 March 2014
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@@ Line 33: / Line 33: @@
 # fetch them at once, load them into PyMOL all at once (synchronously)
 fetch 1kao 1ctq, async=0
 # Example loading a protein and its electron density map