Biological Unit: Showing: Difference between revisions
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This article explains how to show a biological unit (biological assembly) from a green link in a scene in Proteopedia. If you simply want to see a biological unit, go to [[Biological Unit#Visualizing the Biological Unit|Visualizing the Biological Unit]]. For background, see [[Biological Unit]] and [[Asymmetric Unit]]. | This article explains how to show a biological unit (biological assembly) from a green link in a scene in Proteopedia. If you simply want to see a biological unit, go to [[Biological Unit#Visualizing the Biological Unit|Visualizing the Biological Unit]]. For background, see [[Biological Unit]] and [[Asymmetric Unit]]. | ||
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The filter used by FirstGlance, and in fact the entire load command, can be displayed by clicking ''Troubleshooting'' below the molecule. Then, scroll down to the bottom in the ''Troubleshooting'' (lower left) panel. Here is the report for 7r1c: | The filter used by FirstGlance, and in fact the entire load command, can be displayed by clicking ''Troubleshooting'' below the molecule. Then, scroll down to the bottom in the ''Troubleshooting'' (lower left) panel. Here is the report for 7r1c: | ||
The Jmol command that loaded this file was: | The Jmol command that loaded this file was: | ||
load MODELS ({0}) https://files.rcsb.org/download/7R1C.pdb filter | |||
"!_H;*.CA;*.P;%A;ALLHET;biomolecule 3;bmchains;/=3"; delete water;delete hydrogen; | |||
Here is an explanation: | Here is an explanation: | ||
* MODELS ({0}) -- When multiple models are present in the PDB file, only the first model is loaded, regardless of whether that model is assigned number 1 (typical) or another number, such as number 0 (AlphaFold). When the PDB file contains only a single model, this has no effect. | * MODELS ({0}) -- When multiple models are present in the PDB file, only the first model is loaded, regardless of whether that model is assigned number 1 (typical) or another number, such as number 0 (AlphaFold). When the PDB file contains only a single model, this has no effect. | ||
* !_H | * !_H; Do not load hydrogen atoms. | ||
* *.CA; Load only alpha carbon atoms for proteins. | |||
* *. | * *.P; Load only backbone phosphorus atoms for nucleic acids. | ||
* | * %A; When some atoms have [[alternate locations]], load only their first location. This avoids having multiple copies of the same atom in different locations. | ||
* | * ALLHET; Load all [[hetero atoms]] (ligands). In addition to ligands, this loads the hydrogen atoms that are part of ligands or other hetero moieties, and it loads water. | ||
* | * biomolecule 3; This constructs and loads biological unit (assembly) number 3 specified in the PDB file. | ||
* biomolecule | * bmchains; When some chains are duplicated to construct the biomolecule, each chain is given a distinct name. For example, 3hyd contains a singe chain A in its asymmetric unit, and 4 chains in biomolecule 1. The additional chains are named A2, A3, and A4. These are not legal chain names in PDB format, which restricts chain names to a single character. However, they work internally within JSmol and FirstGlance is adapted to handle them correctly. To see the complete list of chain names, click on the count of chains in the [http://firstglance.jmol.org/notes.htm#mit Molecule Information Tab] of FirstGlance. | ||
* | * /=3; This loads only every third alpha carbon or nucleic backbone phosphorus atom. | ||
* | * delete water; This deletes all water that was loaded due to ALLHET. | ||
* delete | * delete hydrogen; This deletes ligand hydrogen atoms that were loaded due to ALLHET. | ||
* | ==See Also== | ||
*[[Scene_authoring_tools#.27load_molecule.27_tab|Scene authoring tools: 'load molecule' tab]] | |||