Biological Unit: Showing: Difference between revisions
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When the number of alpha carbons exceeds about 30,000, JSmol will perform much better if only a subset of the alpha carbon atoms are loaded. To load only every 3rd alpha carbon, put '''/=3''' at the end of the FILTER. So the complete FILTER could be, for example, '''*.CA;biomolecule 3;/=3;'''. | When the number of alpha carbons exceeds about 30,000, JSmol will perform much better if only a subset of the alpha carbon atoms are loaded. To load only every 3rd alpha carbon, put '''/=3''' at the end of the FILTER. So the complete FILTER could be, for example, '''*.CA;biomolecule 3;/=3;'''. | ||
==Loading Filters== | |||
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: | |||
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: | |||
* 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 -- 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). This loads the hydrogen atoms that are part of hetero atoms. | |||