Jmol/Visualizing large molecules: Difference between revisions
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==Biological Assemblies== | ==Biological Assemblies== | ||
The functional forms of molecules, often called [[biological unit|biological units]] or [[biological unit|biological assemblies]], may contain many copies of the chains present in the published PDB file (the [[asymmetric unit]]). An extreme example is a virus capsid. The capsid of the Simian Virus 40 contains 360 copies of the VP1 protein chain, present in | The functional forms of molecules, often called [[biological unit|biological units]] or [[biological unit|biological assemblies]], may contain many copies of the chains present in the published PDB file (the [[asymmetric unit]]). | ||
===Virus Capsids=== | |||
An extreme example is a virus capsid. The capsid of the Simian Virus 40 (SV40) contains 360 copies of the VP1 protein chain, present in 6 copies in the published PDB file [[1sva]]. An extremely simplified model of the capsid is displayed at [[SV40_Capsid_Simplified]], but this model required special techniques to construct. We can get the full capsid model from any of [[biological unit|several servers]]. For reasons explained [[biological unit|there]], the most useful model is obtained from the MakeMultimers server. The full capsid model (360 copies of the VP1 protein chain, minus hydrogen atoms) is a PDB file of 70 megabytes, too large for default java/Jmol memory. Below are instructions for getting the much smaller alpha carbon atom model. | |||
===SV40 Capsid Alpha Carbons=== | |||
