Biological Unit - Revision history

Eric Martz: /* Proteopedia */

Eric Martz — Sat, 12 Nov 2022 19:04:54 GMT

Proteopedia

←Older revision		Revision as of 19:04, 12 November 2022
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	===Proteopedia===		===Proteopedia===
-	On pages titled with a [[PDB code]], Proteopedia shows biological unit 1 by default, with an option to show the asymmetric unit instead. A simple example is [[3hyd]]: biological unit 1 has 4 small peptide chains, while the asymmetric unit has a single chain. A large example is [[1pov]], the polio virus capsid. When biological unit 1 becomes too large for JSmol to handle effectively, it is displayed in [[Molstar\|Mol*]] ("[[Molstar]]") instead of JSmol. An example is the much larger capsid of Eastern Equine Encephalitis Virus, [[6mx4]].	+	On pages titled with a [[PDB code]], Proteopedia shows biological unit 1 by default, with an option to show the asymmetric unit instead. A simple example is [[3hyd]]: biological unit 1 has 4 small peptide chains, while the asymmetric unit has a single chain. A large example is [[1pov]], the polio virus capsid. When biological unit 1 becomes too large for JSmol to handle effectively, it is displayed in [[Molstar\|Mol*]] ("[[Molstar]]") instead of [[JSmol]]. An example is the much larger capsid of Eastern Equine Encephalitis Virus, [[6mx4]].

	===FirstGlance in Jmol===		===FirstGlance in Jmol===

Eric Martz: /* Proteopedia */

Eric Martz — Sat, 12 Nov 2022 19:04:37 GMT

Proteopedia

←Older revision		Revision as of 19:04, 12 November 2022
Line 76:		Line 76:

	===Proteopedia===		===Proteopedia===
-	On pages titled with a [[PDB code]], Proteopedia shows biological unit 1 by default, with an option to show the asymmetric unit instead. A simple example is [[3hyd]]: biological unit 1 has 4 small peptide chains, while the asymmetric unit has a single chain. A large example is [[1pov]], the polio virus capsid. When biological unit 1 becomes too large for JSmol to handle effectively, it is displayed in [[Molstar\|Mol*]] ("Molstar") instead of JSmol. An example is the much larger capsid of Eastern Equine Encephalitis Virus, [[6mx4]].	+	On pages titled with a [[PDB code]], Proteopedia shows biological unit 1 by default, with an option to show the asymmetric unit instead. A simple example is [[3hyd]]: biological unit 1 has 4 small peptide chains, while the asymmetric unit has a single chain. A large example is [[1pov]], the polio virus capsid. When biological unit 1 becomes too large for JSmol to handle effectively, it is displayed in [[Molstar\|Mol*]] ("[[Molstar]]") instead of JSmol. An example is the much larger capsid of Eastern Equine Encephalitis Virus, [[6mx4]].

	===FirstGlance in Jmol===		===FirstGlance in Jmol===

Eric Martz: /* Proteopedia */

Eric Martz — Sat, 12 Nov 2022 19:04:15 GMT

Proteopedia

←Older revision		Revision as of 19:04, 12 November 2022
Line 76:		Line 76:

	===Proteopedia===		===Proteopedia===
-	On pages titled with a [[PDB code]], Proteopedia shows biological unit 1 by default, with an option to show the asymmetric unit instead. A simple example is [[3hyd]]: biological unit 1 has 4 small peptide chains, while the asymmetric unit has a single chain. A large example is [[1pov]], the polio virus capsid. When biological unit 1 becomes too large for JSmol to handle effectively, it is displayed in ~~@@@@@@~~ instead of JSmol. An example is the much larger capsid of Eastern Equine Encephalitis Virus, [[6mx4]].	+	On pages titled with a [[PDB code]], Proteopedia shows biological unit 1 by default, with an option to show the asymmetric unit instead. A simple example is [[3hyd]]: biological unit 1 has 4 small peptide chains, while the asymmetric unit has a single chain. A large example is [[1pov]], the polio virus capsid. When biological unit 1 becomes too large for JSmol to handle effectively, it is displayed in [[Molstar\|Mol*]] ("Molstar") instead of JSmol. An example is the much larger capsid of Eastern Equine Encephalitis Virus, [[6mx4]].

	===FirstGlance in Jmol===		===FirstGlance in Jmol===

Eric Martz: /* FirstGlance in Jmol */

Eric Martz — Sat, 12 Nov 2022 18:17:26 GMT

FirstGlance in Jmol

←Older revision		Revision as of 18:17, 12 November 2022
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	**Enter the [[PDB code]] in the top search slot at the left edge of any page in Proteopedia. At the page in Proteopedia titled with the PDB code, under <i>Resources</i>, click on the link to FirstGlance.		**Enter the [[PDB code]] in the top search slot at the left edge of any page in Proteopedia. At the page in Proteopedia titled with the PDB code, under <i>Resources</i>, click on the link to FirstGlance.
	**Alternatively, go directly to [http://firstglance.jmol.org FirstGlance.Jmol.Org] (google ''firstglance'', one word with no space) and enter the PDB code.		**Alternatively, go directly to [http://firstglance.jmol.org FirstGlance.Jmol.Org] (google ''firstglance'', one word with no space) and enter the PDB code.
-	*In the <i>Molecule Information</i> tab (the first/left-most tab), click <i>Biological Unit</i> and follow instructions.	+	*In the <i>Molecule Information</i> tab (the first/left-most tab), click <i>Biological Unit</i> and follow instructions. When there is more than one biological unit, all will be listed and you can display and analyze each of them.

	===How To Show The Biological Unit In Proteopedia===		===How To Show The Biological Unit In Proteopedia===

Eric Martz: /* =Proteopedia */

Eric Martz — Sat, 12 Nov 2022 18:08:23 GMT

=Proteopedia

←Older revision		Revision as of 18:08, 12 November 2022
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	==Visualizing the Biological Unit==		==Visualizing the Biological Unit==

-	===Proteopedia==	+	===Proteopedia===
	On pages titled with a [[PDB code]], Proteopedia shows biological unit 1 by default, with an option to show the asymmetric unit instead. A simple example is [[3hyd]]: biological unit 1 has 4 small peptide chains, while the asymmetric unit has a single chain. A large example is [[1pov]], the polio virus capsid. When biological unit 1 becomes too large for JSmol to handle effectively, it is displayed in @@@@@@ instead of JSmol. An example is the much larger capsid of Eastern Equine Encephalitis Virus, [[6mx4]].		On pages titled with a [[PDB code]], Proteopedia shows biological unit 1 by default, with an option to show the asymmetric unit instead. A simple example is [[3hyd]]: biological unit 1 has 4 small peptide chains, while the asymmetric unit has a single chain. A large example is [[1pov]], the polio virus capsid. When biological unit 1 becomes too large for JSmol to handle effectively, it is displayed in @@@@@@ instead of JSmol. An example is the much larger capsid of Eastern Equine Encephalitis Virus, [[6mx4]].

Eric Martz: /* Visualizing the Biological Unit */

Eric Martz — Sat, 12 Nov 2022 18:07:44 GMT

Visualizing the Biological Unit

←Older revision		Revision as of 18:07, 12 November 2022
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	<br clear="left">		<br clear="left">
	==Visualizing the Biological Unit==		==Visualizing the Biological Unit==
		+
		+	===Proteopedia==
		+	On pages titled with a [[PDB code]], Proteopedia shows biological unit 1 by default, with an option to show the asymmetric unit instead. A simple example is [[3hyd]]: biological unit 1 has 4 small peptide chains, while the asymmetric unit has a single chain. A large example is [[1pov]], the polio virus capsid. When biological unit 1 becomes too large for JSmol to handle effectively, it is displayed in @@@@@@ instead of JSmol. An example is the much larger capsid of Eastern Equine Encephalitis Virus, [[6mx4]].
		+
	===FirstGlance in Jmol===		===FirstGlance in Jmol===
	FirstGlance in Jmol makes it quick and easy to see, explore, and analyze the biological unit. The initial display in FirstGlance is automatically "biomolecule 1" from REMARK 350. When it is very large, it will be [http://firstglance.jmol.org/notes.htm#simplification simplified to alpha carbon atoms (or a subset thereof)] automatically by FirstGlance.		FirstGlance in Jmol makes it quick and easy to see, explore, and analyze the biological unit. The initial display in FirstGlance is automatically "biomolecule 1" from REMARK 350. When it is very large, it will be [http://firstglance.jmol.org/notes.htm#simplification simplified to alpha carbon atoms (or a subset thereof)] automatically by FirstGlance.

Eric Martz: /* FirstGlance in Jmol */

Eric Martz — Thu, 10 Nov 2022 21:00:31 GMT

FirstGlance in Jmol

←Older revision		Revision as of 21:00, 10 November 2022
Line 75:		Line 75:
	==Visualizing the Biological Unit==		==Visualizing the Biological Unit==
	===FirstGlance in Jmol===		===FirstGlance in Jmol===
-	FirstGlance in Jmol makes it quick and easy to see the biological unit. The initial display in FirstGlance is automatically "biomolecule 1" from REMARK 350. When it is very large, it will be [http://firstglance.jmol.org/notes.htm#simplification simplified to alpha carbon atoms (or a subset thereof)] automatically by FirstGlance.	+	FirstGlance in Jmol makes it quick and easy to see, explore, and analyze the biological unit. The initial display in FirstGlance is automatically "biomolecule 1" from REMARK 350. When it is very large, it will be [http://firstglance.jmol.org/notes.htm#simplification simplified to alpha carbon atoms (or a subset thereof)] automatically by FirstGlance.
	*Display the molecule in FirstGlance in Jmol:		*Display the molecule in FirstGlance in Jmol:
	**Enter the [[PDB code]] in the top search slot at the left edge of any page in Proteopedia. At the page in Proteopedia titled with the PDB code, under <i>Resources</i>, click on the link to FirstGlance.		**Enter the [[PDB code]] in the top search slot at the left edge of any page in Proteopedia. At the page in Proteopedia titled with the PDB code, under <i>Resources</i>, click on the link to FirstGlance.

Eric Martz: /* FirstGlance in Jmol */

Eric Martz — Thu, 10 Nov 2022 21:00:01 GMT

FirstGlance in Jmol

←Older revision		Revision as of 21:00, 10 November 2022
Line 75:		Line 75:
	==Visualizing the Biological Unit==		==Visualizing the Biological Unit==
	===FirstGlance in Jmol===		===FirstGlance in Jmol===
-	FirstGlance in Jmol makes it quick and easy to see the biological unit. The initial display in FirstGlance is automatically "biomolecule 1" from REMARK 350. When it is very large, it will be ~~automatically~~ [http://firstglance.jmol.org/notes.htm#simplification simplified to alpha carbon atoms (or a subset thereof)] automatically by FirstGlance.	+	FirstGlance in Jmol makes it quick and easy to see the biological unit. The initial display in FirstGlance is automatically "biomolecule 1" from REMARK 350. When it is very large, it will be [http://firstglance.jmol.org/notes.htm#simplification simplified to alpha carbon atoms (or a subset thereof)] automatically by FirstGlance.
	*Display the molecule in FirstGlance in Jmol:		*Display the molecule in FirstGlance in Jmol:
	**Enter the [[PDB code]] in the top search slot at the left edge of any page in Proteopedia. At the page in Proteopedia titled with the PDB code, under <i>Resources</i>, click on the link to FirstGlance.		**Enter the [[PDB code]] in the top search slot at the left edge of any page in Proteopedia. At the page in Proteopedia titled with the PDB code, under <i>Resources</i>, click on the link to FirstGlance.

Eric Martz: /* FirstGlance in Jmol */

Eric Martz — Thu, 10 Nov 2022 20:59:25 GMT

FirstGlance in Jmol

←Older revision		Revision as of 20:59, 10 November 2022
Line 76:		Line 76:
	===FirstGlance in Jmol===		===FirstGlance in Jmol===
	FirstGlance in Jmol makes it quick and easy to see the biological unit. The initial display in FirstGlance is automatically "biomolecule 1" from REMARK 350. When it is very large, it will be automatically [http://firstglance.jmol.org/notes.htm#simplification simplified to alpha carbon atoms (or a subset thereof)] automatically by FirstGlance.		FirstGlance in Jmol makes it quick and easy to see the biological unit. The initial display in FirstGlance is automatically "biomolecule 1" from REMARK 350. When it is very large, it will be automatically [http://firstglance.jmol.org/notes.htm#simplification simplified to alpha carbon atoms (or a subset thereof)] automatically by FirstGlance.
-	#Display the molecule in FirstGlance in Jmol:	+	*Display the molecule in FirstGlance in Jmol:
-	##Enter the [[PDB code]] in the top search slot at the left edge of any page in Proteopedia. At the page in Proteopedia titled with the PDB code, under <i>Resources</i>, click on the link to FirstGlance.	+	**Enter the [[PDB code]] in the top search slot at the left edge of any page in Proteopedia. At the page in Proteopedia titled with the PDB code, under <i>Resources</i>, click on the link to FirstGlance.
-	##Alternatively, go directly to [http://firstglance.jmol.org FirstGlance.Jmol.Org] (google ''firstglance'', one word with no space) and enter the PDB code.	+	**Alternatively, go directly to [http://firstglance.jmol.org FirstGlance.Jmol.Org] (google ''firstglance'', one word with no space) and enter the PDB code.
-	#In the <i>Molecule Information</i> tab (the first/left-most tab), click <i>Biological Unit</i> and follow instructions.	+	*In the <i>Molecule Information</i> tab (the first/left-most tab), click <i>Biological Unit</i> and follow instructions.

	===How To Show The Biological Unit In Proteopedia===		===How To Show The Biological Unit In Proteopedia===

Eric Martz at 20:58, 10 November 2022

Eric Martz — Thu, 10 Nov 2022 20:58:35 GMT

←Older revision		Revision as of 20:58, 10 November 2022
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	Truncated proteins may form oligomers that are impossible in the native protein. For example, [[1bk5]] (karyopherin alpha) is a truncated part of the natural chain, and forms a dimer that would be prevented by the full-length chain. Dimerization is dependent upon Y397. Mutation Y397D prevents this artifactual dimerization, leading to the monomer [[1ee5]].		Truncated proteins may form oligomers that are impossible in the native protein. For example, [[1bk5]] (karyopherin alpha) is a truncated part of the natural chain, and forms a dimer that would be prevented by the full-length chain. Dimerization is dependent upon Y397. Mutation Y397D prevents this artifactual dimerization, leading to the monomer [[1ee5]].

-	==Visualizing the Biological Unit==
	<br clear="left">		<br clear="left">
		+	==Visualizing the Biological Unit==
	===FirstGlance in Jmol===		===FirstGlance in Jmol===
	FirstGlance in Jmol makes it quick and easy to see the biological unit. The initial display in FirstGlance is automatically "biomolecule 1" from REMARK 350. When it is very large, it will be automatically [http://firstglance.jmol.org/notes.htm#simplification simplified to alpha carbon atoms (or a subset thereof)] automatically by FirstGlance.		FirstGlance in Jmol makes it quick and easy to see the biological unit. The initial display in FirstGlance is automatically "biomolecule 1" from REMARK 350. When it is very large, it will be automatically [http://firstglance.jmol.org/notes.htm#simplification simplified to alpha carbon atoms (or a subset thereof)] automatically by FirstGlance.