Jmol/Superposition: Difference between revisions
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| Line 42: | Line 42: | ||
select ~actnagal | select ~actnagal | ||
show selected</nowiki> | show selected</nowiki> | ||
Here is the output: | |||
<nowiki> | |||
structure 1 structure 2 | |||
13 atoms selected 13 atoms selected | |||
[TRP]47:A.CA/1.1 #119 [TRP]33:A.CA/2.1 #115 | |||
[ASP]92:A.CA/1.1 #489 [ASP]78:A.CA/2.1 #496 | |||
[ASP]93:A.CA/1.1 #497 [ASP]79:A.CA/2.1 #504 | |||
[TYR]134:A.CA/1.1 #826 [TYR]119:A.CA/2.1 #814 | |||
[CYS]142:A.CA/1.1 #886 [CYS]127:A.CA/2.1 #877 | |||
[LYS]168:A.CA/1.1 #1086 [LYS]154:A.CA/2.1 #1088 | |||
[ASP]170:A.CA/1.1 #1106 [ASP]156:A.CA/2.1 #1105 | |||
[CYS]172:A.CA/1.1 #1118 [CYS]158:A.CA/2.1 #1117 | |||
[GLU]203:A.CA/1.1 #1358 [SER]188:A.CA/2.1 #1338 | |||
[LEU]206:A.CA/1.1 #1388 [ALA]191:A.CA/2.1 #1365 | |||
[TYR]207:A.CA/1.1 #1396 [TYR]192:A.CA/2.1 #1370 | |||
[ARG]227:A.CA/1.1 #1587 [ARG]213:A.CA/2.1 #1550 | |||
[ASP]231:A.CA/1.1 #1622 [ASP]217:A.CA/2.1 #1589 | |||
</nowiki> | |||
It shows that even though the residue numbers are different within the pairs, most pairs have matching residue types, supporting the notion that atoms are indeed equivalent. (Exceptions are Glu203 vs Ser188, and Leu206 vs Ala 191, which do occupy equivalent positions in the active site but are responsible for different substrate specificities of the two enzymes). This method is excellent for spotting problems like typos, problems related to missing residues in one or the other structure, alternate conformations (i.e. selecting two C-alpha atoms for a single residue), etc. | |||
==Demonstration== | ==Demonstration== | ||
