Selection Macros - Revision history

Cchem: 1 revision

2017-12-11T04:50:19Z

1 revision

Speleo3: syntax, screenshot

2017-11-29T10:19:04Z

syntax, screenshot

Bell: 8 revisions

2014-03-28T03:49:40Z

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Speleo3: adjust indent

2010-09-07T11:23:15Z

adjust indent

Speleo3: slash missing in last example

2010-09-07T11:21:46Z

slash missing in last example

New page

==Selection Macros==
===General===
Macros make it possible to represent a long atom selection phrase such as

<source lang="python">
PyMOL> select pept and segi lig and chain b and resi 142 and name ca
</source>

in a more compact form:

<source lang="python">
PyMOL> select /pept/lig/b/142/ca
</source>

An atom selection macro uses slashes to define fields corresponding to identifiers. The macro is used to select atoms using the boolean "and," that is, the selected atoms must have all the matching identifiers:

<source lang="python">
/object-name/segi-identifier/chain-identifier/resi-identifier/name-identifier
</source>

These identifiers form a hierarchy from the object-name at the top, down to the name-identifier at the bottom. PyMOL has to be able to recognize the macro as one word, so no spaces are allowed within it.

Macros come in two flavors: those that begin with a slash and those that don't. The presence or absence of a slash at the beginning of the macro determines how it is interpreted. If the macro begins with a slash, PyMOL expects to find the fields starting from the top of the hierarchy: the first field to the right of the slash is interpreted as an object-name; the second field as an identifier to segi; the third as an identifier to chain, and so on. It may take any of the following forms:

===Macros Beginning With a Slash===
<pre>
/object-name/segi-identifier/chain-identifier/resi-identifier/name-identifier
/object-name/segi-identifier/chain-identifier/resi-identifier
/object-name/segi-identifier/chain-identifier
/object-name/segi-identifier
/object-name

EXAMPLES
PyMOL> zoom /pept
PyMOL> show spheres, /pept/lig/
PyMOL> show cartoon, /pept/lig/a
PyMOL> color pink, /pept/lig/a/10
PyMOL> color yellow, /pept/lig/a/10/ca
</pre>

===Macros Not Beginning With a Slash===
If the macro does not begin with a slash, it is interpreted differently. In this case, PyMOL expects to find the fields ending with the bottom of the hierarchy. Macros that don't start with a slash may take the following forms:
<pre>
resi-identifier/name-identifier
chain-identifier/resi-identifier/name-identifier
segi-identifier/chain-identifier/resi-identifier/name-identifier
object-name/segi-identifier/chain-identifier/resi-identifier/name-identifier

EXAMPLES
PyMOL> zoom 10/cb
PyMOL> show spheres, a/10-12/ca
PyMOL> show cartoon, lig/b/6+8/c+o
PyMOL> color pink, pept/enz/c/3/n
</pre>

===Omitting Fields in a Macro===
You can also omit fields between slashes. Omitted fields will be interpreted as wildcards, as in the following forms:

<pre>
resi-identifier/
resi-identifier/name-identifier
chain-identifier//
object-name//chain-identifier

EXAMPLES
PyMOL> zoom 142/ # Residue 142 fills the viewer.

PyMOL> show spheres, 156/ca # The alpha carbon of residue 156
# is shown as a sphere

PyMOL> show cartoon, a// # Chain "A" is shown as a cartoon.

PyMOL> color pink, /pept//b # Chain "B" in object "pept"
# is colored pink.
</pre>

Selection macros must contain at least one forward slash in order to distinguish them from other words in the selection language. Being words, they must not contain any spaces. When using macros, it is also important to understand that they are converted into long form before being submitted to the selection engine. This can help in the interpretation of error messages.

[[Category:Selector Quick Reference]]
[[Category:Selecting|Selection Macros]]
[[Category:Coloring]]

Jcorn: /* Selection Macros */

2005-02-21T00:44:56Z

Selection Macros

Jcorn at 00:42, 21 February 2005

2005-02-21T00:42:10Z

Jcorn at 00:38, 21 February 2005

2005-02-21T00:38:58Z

New page

==Selection Macros==
===General===
Macros make it possible to represent a long atom selection phrase such as

<pre>PyMOL> select pept and segi lig and chain b and resi 142 and name ca</pre>

in a more compact form:

<pre>PyMOL> select /pept/lig/b/142/ca</pre>

An atom selection macro uses slashes to define fields corresponding to identifiers. The macro is used to select atoms using the boolean "and," that is, the selected atoms must have all the matching identifiers:

<pre> /object-name/segi-identifier/chain-identifier/resi-identifier/name-identifier</pre>

These identifiers form a hierarchy from the object-name at the top, down to the name-identifier at the bottom. PyMOL has to be able to recognize the macro as one word, so no spaces are allowed within it.

Macros come in two flavors: those that begin with a slash and those that don't. The presence or absence of a slash at the beginning of the macro determines how it is interpreted. If the macro begins with a slash, PyMOL expects to find the fields starting from the top of the hierarchy: the first field to the right of the slash is interpreted as an object-name; the second field as an identifier to segi; the third as an identifier to chain, and so on. It may take any of the following forms:

===Macros Beginning With a Slash===
<pre>
/object-name/segi-identifier/chain-identifier/resi-identifier/name-identifier
/object-name/segi-identifier/chain-identifier/resi-identifier
/object-name/segi-identifier/chain-identifier
/object-name/segi-identifier
/object-name

EXAMPLES
PyMOL> zoom /pept
PyMOL> show spheres, /pept/lig/
PyMOL> show cartoon, /pept/lig/a
PyMOL> color pink, /pept/lig/a/10
PyMOL> color yellow, /pept/lig/a/10/ca
</pre>

===Macros Not Beginning With a Slash===
If the macro does not begin with a slash, it is interpreted differently. In this case, PyMOL expects to find the fields ending with the bottom of the hierarchy. Macros that don't start with a slash may take the following forms:
<pre>
resi-identifier/name-identifier
chain-identifier/resi-identifier/name-identifier
segi-identifier/chain-identifier/resi-identifier/name-identifier
object-name/segi-identifier/chain-identifier/resi-identifier/name-identifier

EXAMPLES
PyMOL> zoom 10/cb
PyMOL> show spheres, a/10-12/ca
PyMOL> show cartoon, lig/b/6+8/c+o
PyMOL> color pink, pept/enz/c/3/n
</pre>

===Omitting Fields in a Macro===
You can also omit fields between slashes. Omitted fields will be interpreted as wildcards, as in the following forms:

<pre>
resi-identifier/
resi-identifier/name-identifier
chain-identifier//
object-name//chain-identifier

EXAMPLES
PyMOL> zoom 142/ # Residue 142 fills the viewer.

PyMOL> show spheres, 156/ca # The alpha carbon of residue 156
# is shown as a sphere

PyMOL> show cartoon, a// # Chain "A" is shown as a cartoon.

PyMOL> color pink, pept//b # Chain "B" in object "pept"
# is colored pink.
</pre>

Selection macros must contain at least one forward slash in order to distinguish them from other words in the selection language. Being words, they must not contain any spaces. When using macros, it is also important to understand that they are converted into long form before being submitted to the selection engine. This can help in the interpretation of error messages.

[[Category:Selection Macros]]

← Older revision		Revision as of 00:44, 21 February 2005
Line 79:		Line 79:

	[[Category:Selector Quick Reference]]		[[Category:Selector Quick Reference]]
		+
		+	[[Category:Making Selections]]

← Older revision		Revision as of 00:42, 21 February 2005
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−	[[Category:~~Selection Macros~~]]	+	[[Category:Selector Quick Reference]]

← Older revision	Revision as of 04:50, 11 December 2017
(No difference)

@@ Line 1: / Line 1: @@
-==Selection Macros==
+[[Image:right-click-macro.png|right|frame|The atom-right-click context menu title shows a selection macro]]
-===General===
-Macros make it possible to represent a long atom selection phrase such as
+[[Selection Macros]] allow to represent a long [[Selection Algebra|atom selection]] phrase such as
-<source lang="python">
+ PyMOL> select pept and segi lig and chain B and resi 142 and name CA
 in a more compact form:
-<source lang="python">
+ PyMOL> select /pept/lig/B/142/CA
-PyMOL> select /pept/lig/b/142/ca
-</source>
+== Syntax and Semantics ==
 An atom selection macro uses slashes to define fields corresponding to identifiers. The macro is used to select atoms using the boolean "and," that is, the selected atoms must have all the matching identifiers:
@@ Line 19: / Line 17: @@
 </source>
-These identifiers form a hierarchy from the object-name at the top, down to the name-identifier at the bottom. PyMOL has to be able to recognize the macro as one word, so no spaces are allowed within it.
+* must contain '''at least one slash'''
 Macros come in two flavors: those that begin with a slash and those that don't. The presence or absence of a slash at the beginning of the macro determines how it is interpreted. If the macro begins with a slash, PyMOL expects to find the fields starting from the top of the hierarchy: the first field to the right of the slash is interpreted as an object-name; the second field as an identifier to segi; the third as an identifier to chain, and so on. It may take any of the following forms:
@@ Line 35: / Line 40: @@
     PyMOL> zoom /pept
     PyMOL> show spheres, /pept/lig/
-    PyMOL> show cartoon, /pept/lig/a
+    PyMOL> show cartoon, /pept/lig/A
-    PyMOL> color pink, /pept/lig/a/10
+    PyMOL> color pink, /pept/lig/A/10
-    PyMOL> color yellow, /pept/lig/a/10/ca
+    PyMOL> color yellow, /pept/lig/A/10/CA
 </pre>
@@ Line 50: / Line 55: @@
 EXAMPLES
-    PyMOL> zoom 10/cb
+    PyMOL> zoom 10/CB
-    PyMOL> show spheres, a/10-12/ca
+    PyMOL> show spheres, A/10-12/CB
-    PyMOL> show cartoon, lig/b/6+8/c+o
+    PyMOL> show cartoon, lig/B/6+8/C+O
-    PyMOL> color pink, pept/enz/c/3/n
+    PyMOL> color pink, pept/enz/C/3/N
 </pre>
 ===Omitting Fields in a Macro===
@@ Line 70: / Line 74: @@
     PyMOL> zoom 142/                  # Residue 142 fills the viewer.
-    PyMOL> show spheres, 156/ca       # The alpha carbon of residue 156
+    PyMOL> show spheres, 156/CA       # The alpha carbon of residue 156
                                       # is shown as a sphere
-    PyMOL> show cartoon, a//          # Chain "A" is shown as a cartoon.
+    PyMOL> show cartoon, A//          # Chain "A" is shown as a cartoon.
-    PyMOL> color pink, /pept//b       # Chain "B" in object "pept"
+    PyMOL> color pink, /pept//B       # Chain "B" in object "pept"
                                       # is colored pink.
 </pre>
+* [[Selection Algebra]]
 [[Category:Selector Quick Reference]]
 [[Category:Selecting|Selection Macros]]
 [[Category:Coloring]]

← Older revision	Revision as of 03:49, 28 March 2014
(No difference)