How to's - Revision history

Dave at 16:02, 6 June 2014

2014-06-06T16:02:12Z

Dave at 10:47, 18 October 2013

2013-10-18T10:47:11Z

← Older revision		Revision as of 10:47, 18 October 2013
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	''Basic building blocks of the language - i.e. atoms, residues, and the like.''		''Basic building blocks of the language - i.e. atoms, residues, and the like.''
	=== AminoAcids ===		=== AminoAcids ===
	<code>AminoAcids -> Residues</code><br/>		<code>AminoAcids() -> Residues</code><br/>
	''Sequence of all amino acids in a given protein.''<br/>		''Sequence of all amino acids in a given protein.''<br/>
	;Options		;Options
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	----		----
	=== NotAminoAcids ===		=== NotAminoAcids ===
	<code>NotAminoAcids -> Residues</code><br/>		<code>NotAminoAcids() -> Residues</code><br/>
	''Sequence of all residues resudies that are not amino acids.''<br/>		''Sequence of all residues resudies that are not amino acids.''<br/>
	;Options		;Options
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	----		----
	=== CSA ===		=== CSA ===
	<code>CSA -> Motives</code><br/>		<code>CSA() -> Motives</code><br/>
	''Entries from Catalytic Site Atlas represented as motifs. Works only if used from the command line version of MotiveQuery and property configured.''<br/>		''Entries from Catalytic Site Atlas represented as motifs. Works only if used from the command line version of MotiveQuery and property configured.''<br/>
	<small>''Note:'' This function cannot be used directly to query motifs from MotiveExplorer or MotiveQuery service.</small><br/>		<small>''Note:'' This function cannot be used directly to query motifs from MotiveExplorer or MotiveQuery service.</small><br/>
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	----		----
	=== Current ===		=== Current ===
	<code>Current -> Motive</code><br/>		<code>Current() -> Motive</code><br/>
	''A variable that is assigned by the application environment.''<br/>		''A variable that is assigned by the application environment.''<br/>
	<small>''Note:'' This function cannot be used directly to query motifs from MotiveExplorer or MotiveQuery service.</small><br/>		<small>''Note:'' This function cannot be used directly to query motifs from MotiveExplorer or MotiveQuery service.</small><br/>

Dave at 10:43, 18 October 2013

2013-10-18T10:43:15Z

Show changes

Dave: Created page with "== SiteBinder == === Select all structures that have exactly one C₅O ring === Enter `Current().Count(Rings(5 * ["C"] + ["O"])) == 1` into the Structure..."

2013-06-07T03:20:44Z

Created page with "== SiteBinder == === Select all structures that have exactly one C5O ring === Enter <code>Current().Count(Rings(5 * ["C"] + ["O"])) == 1</code> into the Structure..."

New page

== SiteBinder ==

=== Select all structures that have exactly one C5O ring ===

Enter <code>Current().Count(Rings(5 * ["C"] + ["O"])) == 1</code> into the Structure Selection panel.

Explanation:

# <code>Current()</code> returns the structure being tested.
# <code>Count()</code> function counts occurrences of a specific motif.
# <code>Rings(5 * ["C"] + ["O"])</code> is a "Python" shortcut for <code>Rings(["C", "C", "C", "C", "C", "O"])</code> which represents a ring with 5 C and 1 O atoms.
# <code> == 1</code> checks for equality. Other relation operators can be used as well ( >, >=, <, <=, !=).

=== Select all structures that satisfy multiple conditions ===

In the Structure Selection panel use the expression <code>(c1) & (c2)</code>. For example, all structures that contain more than one C5O ring and no more than 3 ASP residues is represented by the expression <code>(Current().Count(Rings(5 * ["C"] + ["O"])) > 1) & (Current().Count(Residues("HIS")) <= 3)</code>. Due to the associativity rules of the operator &, each condition must be enclosed in the ( ). Or condition is represented by using | operator instead of &.

=== Select all backbone C atoms that are within 6 angstroms of MAN residue ===

Enter <code>AtomNames("CA", "CB").Inside(Residues("MAN").AmbientAtoms(6))</code> into the Atom Selection panel.

Explanation:

# <code>AtomNames("CA", "CB")</code> represents all atoms names "CA" or "CB".
# <code>.Inside(...)</code> function says that the motive on the left should be looked for inside another one.
# <code>Residues("MAN").AmbientAtoms(6)</code> represents all atoms on a MAN residue and all atoms within 6 angstroms around it.

=== Cluster loaded structures by their common residues ===

Enter <code>Utils.ResidueHierarchialClustering("name")</code> to the script panel. This will create several descriptors for the loaded structures with these properties:

* For each cluster, two descriptors are added:
** <code>name</code>_<code>N</code> – all motifs that share at least N residues. If a motif has less than N residues, large cluster index will be displayed (2^31).
** <code>name</code>_<code>N</code>FP – a list of the common residues. If a motif has less than N residues, “n/a” is displayed.
* Descriptors can be changed using the Structure Descriptors panel.
* There is also an export button in the Structure Descriptors panel.
* Use Group by Descriptor and Sort by Descriptor functions for added effect.

=== Create a descriptor with residue count ===

Enter <code>Current().Count(Residues())</code> and select an appropriate name (say "resCount") in the Descpriptors panel.

Explanation:

# <code>Current()</code> returns the structure we are computing the descriptor for.
# <code>.Count(Residues())</code> counts the residues.

It is possible to count all sorts of things:

* <code>Atoms("C", "N")</code> counts C and N atoms.
* <code>AtomNames("CA", "CB")</code> counts atoms named CA and CB.
* <code>Residues("HIS", "ASP")</code> counts HIS and ASP residues.
* <code>Rings(5 * ["C"] + ["O"])</code> counts C5O rings.

This descriptor can also be expanded and further analyzed for example in Excel using the Export menu in the Descriptors panel.

== MotiveExplorer ==

Seems there is nothing here.

== EEM Charges ==

Seems there is nothing here.

How to's - Revision history

Dave at 16:02, 6 June 2014

Dave at 10:47, 18 October 2013

Dave at 10:43, 18 October 2013

Dave: Created page with "== SiteBinder == === Select all structures that have exactly one C5O ring === Enter Current().Count(Rings(5 * ["C"] + ["O"])) == 1 into the Structure..."

Dave: Created page with "== SiteBinder == === Select all structures that have exactly one C₅O ring === Enter `Current().Count(Rings(5 * ["C"] + ["O"])) == 1` into the Structure..."