Jmol/Superposition: Difference between revisions
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Jmol does not alert you if your sets of equivalent atoms used in a superposition contain different number of atoms. Let's say you made a mistake in your selection and the first atom set contains 50 atoms and the second contains 51. Jmol will just ignore the last atom in the second set. However, your mistake might have messed up the pairing of atoms you intended. The only feedback jmol gives is the so-called RMSD (the root-mean-square distance of equivalent atom pairs). You can also check if your superposition makes sense by displaying both structures, and checking if equivalent atoms are close to each other. | Jmol does not alert you if your sets of equivalent atoms used in a superposition contain different number of atoms. Let's say you made a mistake in your selection and the first atom set contains 50 atoms and the second contains 51. Jmol will just ignore the last atom in the second set. However, your mistake might have messed up the pairing of atoms you intended. The only feedback jmol gives is the so-called RMSD (the root-mean-square distance of equivalent atom pairs). You can also check if your superposition makes sense by displaying both structures, and checking if equivalent atoms are close to each other. | ||
If something did go awry, an efficient way of troubleshooting is to list the selected atoms. | If something did go awry, an efficient way of troubleshooting is to list the selected atoms. Whenever you select atoms, jmol tells you how many atoms are selected. The command "show selection" shows a list of all the selected atoms. If you put both lists side by side, the intended equivalent atom pairs should line up. | ||
<nowiki> | |||
define ~actgal 1.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *.CA:A | |||
define ~actnagal 2.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *.CA:A | |||
select ~actgal | |||
show selected | |||
select ~actnagal | |||
show selected<nowiki> | |||
==Discussion== | ==Discussion== | ||
<StructureSection load='1d9z' size='340' side='right' caption='' scene=''> | <StructureSection load='1d9z' size='340' side='right' caption='' scene=''> | ||
