Alternate locations - Revision history

Eric Martz: /* Visualizing alternate locations */

Eric Martz — Fri, 01 Sep 2023 18:27:41 GMT

Visualizing alternate locations

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-	In May, 2023, FirstGlance in Jmol (version 4.1) handles '''sidechain''' alternate locations well, summarizing alternate location statistics, and offering to animate them. However, it handles '''backbone''' atom alternate locations poorly. It fails to show their existence in the initial view, and cannot animate them. Enhancements to improve handling of backbone atom alternate locations are under development.	+	In May, 2023, FirstGlance in Jmol (version 4.1) handles '''sidechain''' alternate locations well, summarizing alternate location statistics, and offering to animate them. However, it handles '''backbone''' atom alternate locations poorly. It fails to show their existence in the initial view, and cannot animate them. Enhancements to improve handling of backbone atom alternate locations are under development in version 4.2, release expected in fall, 2023.
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Eric Martz: /* Conformations */

Eric Martz — Fri, 01 Sep 2023 18:24:38 GMT

Conformations

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	[[Image:Altloc-animation-9ins.gif\|right]]		[[Image:Altloc-animation-9ins.gif\|right]]
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-	Multiple alternate locations for atoms represent multiple conformations that the ~~model~~ can adopt. (The term ''conformations'' means differences due to rotations of covalent bonds, without removing or adding any covalent bonds. The term ''configurations'' means differences in covalent bonds.) As an example, the tiny protein insulin has 51 amino acids. In [[9ins]] (resolution 1.7 Å), 8 sidechains have 2 alternate locations each (48 atoms, or 10% of its 484 atoms). It is important to realize that movements of these sidechains will mostly be independent of each other. Thus, there could be 2<sup>8</sup> or 256 conformations. In the [[PDB file]], each sidechain location is marked A or B (%A or %B in Jmol language). When FirstGlance animates the alternate locations, for the sake of simplicity, it shows all the A locations together, and then all the B locations together. Note that this is greatly oversimplified, showing 2 conformations instead of 256. And since empirically-determined models are mostly static, while real molecules vibrate, even 256 conformations is an underestimate.	+	Multiple alternate locations for atoms represent multiple conformations that the molecule can adopt. (The term ''conformations'' means differences due to rotations of covalent bonds, without removing or adding any covalent bonds. The term ''configurations'' means differences in covalent bonds.) As an example, the tiny protein insulin has 51 amino acids. In [[9ins]] (resolution 1.7 Å), 8 sidechains have 2 alternate locations each (48 atoms, or 10% of its 484 atoms). It is important to realize that movements of these sidechains will mostly be independent of each other. Thus, there could be 2<sup>8</sup> or 256 conformations. In the [[PDB file]], each sidechain location is marked A or B (%A or %B in Jmol language). When FirstGlance animates the alternate locations, for the sake of simplicity, it shows all the A locations together, and then all the B locations together. Note that this is greatly oversimplified, showing 2 conformations instead of 256. And since empirically-determined models are mostly static, while real molecules vibrate, even 256 conformations is an underestimate.

	==Prevalence of alternate locations==		==Prevalence of alternate locations==

Eric Martz at 18:23, 1 September 2023

Eric Martz — Fri, 01 Sep 2023 18:23:51 GMT

←Older revision		Revision as of 18:23, 1 September 2023
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	with occupancy percentages.		with occupancy percentages.
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-	Many [[Atomic_coordinate_file#PDB_Data_Format\|PDB files]] have '''alternate locations''' (altlocs) for some atoms, marked with an altloc identifier, typically A and B. At sufficiently high [[resolution]], two or more positions may be visible in the [[electron density map]] for certain atoms. If 2 alternate locations have approximately equal densities, each alternate location will be assigned an '''occupancy''' of 50%. Sometimes 3 or even more alternate locations may be distinguished (see examples ~~in the following section~~).	+	Many [[Atomic_coordinate_file#PDB_Data_Format\|PDB files]] have '''alternate locations''' (altlocs) for some atoms, marked with an altloc identifier, typically A and B. At sufficiently high [[resolution]], two or more positions may be visible in the [[electron density map]] for certain atoms. If 2 alternate locations have approximately equal densities, each alternate location will be assigned an '''occupancy''' of 50%. Sometimes 3 or even more alternate locations may be distinguished (see examples below).

	==Conformations==		==Conformations==

Eric Martz at 18:22, 1 September 2023

Eric Martz — Fri, 01 Sep 2023 18:22:52 GMT

←Older revision		Revision as of 18:22, 1 September 2023
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	with occupancy percentages.		with occupancy percentages.
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-	~~Some~~ [[Atomic_coordinate_file#PDB_Data_Format\|PDB files]] have '''alternate locations''' (altlocs) for some atoms~~. Each atom that has altlocs is~~ marked with an altloc identifier, typically A and B. At sufficiently high [[resolution]], two or more positions may be visible in the [[electron density map]] for certain atoms. If 2 alternate locations have approximately equal densities, each alternate location will be assigned an '''occupancy''' of 50%. Sometimes 3 or even more alternate locations may be distinguished (see examples in the following section).	+	Many [[Atomic_coordinate_file#PDB_Data_Format\|PDB files]] have '''alternate locations''' (altlocs) for some atoms, marked with an altloc identifier, typically A and B. At sufficiently high [[resolution]], two or more positions may be visible in the [[electron density map]] for certain atoms. If 2 alternate locations have approximately equal densities, each alternate location will be assigned an '''occupancy''' of 50%. Sometimes 3 or even more alternate locations may be distinguished (see examples in the following section).

	==Conformations==		==Conformations==

Eric Martz at 18:02, 1 September 2023

Eric Martz — Fri, 01 Sep 2023 18:02:36 GMT

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-	<table align="right" width="240"><tr><td>	+	<table align="right" width="240" class="wikitable"><tr><td>
	[[Image:Altloc-arg201-7s99-occ.png]]		[[Image:Altloc-arg201-7s99-occ.png]]
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Eric Martz: /* Visualizing alternate locations */

Eric Martz — Fri, 01 Sep 2023 18:01:04 GMT

Visualizing alternate locations

←Older revision		Revision as of 18:01, 1 September 2023
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	<i>N->C Rainbow</i> view of FirstGlance, colored by conformations. Animation by FirstGlance version 4.2.		<i>N->C Rainbow</i> view of FirstGlance, colored by conformations. Animation by FirstGlance version 4.2.
-	Animation [http://~~firstglance.jmol~~.org/videocapture.htm captured as a GIF].	+	Animation [http://bioinformatics.org/firstglance/fgij/videocapture.htm captured as a GIF].

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Eric Martz: /* Conformations */

Eric Martz — Fri, 01 Sep 2023 18:00:29 GMT

Conformations

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	==Conformations==		==Conformations==
	<table align="right" class="wikitable"><tr><td width="200">		<table align="right" class="wikitable"><tr><td width="200">
-	Two conformations in [[9ins]] animated by [[FirstGlance in Jmol]]. Animation [http://~~firstglance.jmol~~.org/videocapture.htm captured as a GIF].	+	Two conformations in [[9ins]] animated by [[FirstGlance in Jmol]]. Animation [http://bioinformatics.org/firstglance/fgij/videocapture.htm captured as a GIF].

Eric Martz: /* Jmol vs. alternate locations */

Eric Martz — Fri, 01 Sep 2023 17:53:25 GMT

Jmol vs. alternate locations

←Older revision		Revision as of 17:53, 1 September 2023
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	Similarly, Jmol defines '''Conformation 2''' as atoms with no AltLoc codes, atoms with only a single AltLoc code (thus only one location), and the '''second''' location for every atom with an alternate-location code that has multiple locations. This second location may or may not be coded B.		Similarly, Jmol defines '''Conformation 2''' as atoms with no AltLoc codes, atoms with only a single AltLoc code (thus only one location), and the '''second''' location for every atom with an alternate-location code that has multiple locations. This second location may or may not be coded B.

-	[http://firstglance.jmol.org/conformations.htm Details of how FirstGlance defines conformations].	+	[http://firstglance.jmol.org/conformations.htm Details of how FirstGlance defines conformations] (will be available when FirstGlance version 4.2 is released in fall, 2023).

	==Models with the most alternate locations==		==Models with the most alternate locations==

Eric Martz: /* Jmol vs. alternate locations */

Eric Martz — Fri, 01 Sep 2023 17:52:32 GMT

Jmol vs. alternate locations

←Older revision		Revision as of 17:52, 1 September 2023
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	Similarly, Jmol defines '''Conformation 2''' as atoms with no AltLoc codes, atoms with only a single AltLoc code (thus only one location), and the '''second''' location for every atom with an alternate-location code that has multiple locations. This second location may or may not be coded B.		Similarly, Jmol defines '''Conformation 2''' as atoms with no AltLoc codes, atoms with only a single AltLoc code (thus only one location), and the '''second''' location for every atom with an alternate-location code that has multiple locations. This second location may or may not be coded B.
		+
		+	[http://firstglance.jmol.org/conformations.htm Details of how FirstGlance defines conformations].

	==Models with the most alternate locations==		==Models with the most alternate locations==

Eric Martz: /* Visualizing alternate locations */

Eric Martz — Fri, 01 Sep 2023 17:50:42 GMT

Visualizing alternate locations

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	[http://firstglance.jmol.org FirstGlance in Jmol] tells you how many atoms have alternate locations (when you are in ''more details'' mode), and the range of occupancies assigned to them. It tabulates summaries of alternate locations and occupancies, with links that highlight subgroups. It can '''animate''' alternate locations. Examples (from [[FirstGlance in Jmol]]):		[http://firstglance.jmol.org FirstGlance in Jmol] tells you how many atoms have alternate locations (when you are in ''more details'' mode), and the range of occupancies assigned to them. It tabulates summaries of alternate locations and occupancies, with links that highlight subgroups. It can '''animate''' alternate locations. Examples (from [[FirstGlance in Jmol]]):

-	The links below display the model in FirstGlance. Right click the link to open it in a new browser tab. Look in the [http://firstglance.jmol.org/where.htm#mit Molecule Information Tab] ~~for~~ ''alternate locations''.	+	The links below display the model in FirstGlance. Right click the link to open it in a new browser tab. Look in the [http://firstglance.jmol.org/where.htm#mit Molecule Information Tab] to click on ''Show More Details'', then click on ''alternate locations''.

	*Glu3 in [http://firstglance.jmol.org/fg.htm?mol=3hyd 3HYD]. The atom with the largest distance between its alternate locations is the sidechain epsilon oxygen 1 (OE1), with 1.66 Å between alternate locations. Here are its ATOM records from the [[PDB file]]. The vertical bar points to the column with the altloc A and B designators. Each location is assigned 50% occupancy ("Occ" column).		*Glu3 in [http://firstglance.jmol.org/fg.htm?mol=3hyd 3HYD]. The atom with the largest distance between its alternate locations is the sidechain epsilon oxygen 1 (OE1), with 1.66 Å between alternate locations. Here are its ATOM records from the [[PDB file]]. The vertical bar points to the column with the altloc A and B designators. Each location is assigned 50% occupancy ("Occ" column).