Jmol/Visualizing large molecules: Difference between revisions
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===Virus Capsids=== | ===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. | 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. These instructions should work for most virus capsids. | ||
===SV40 Capsid Alpha Carbons=== | ===SV40 Capsid Alpha Carbons=== | ||
*'''Generate The Capsid''': Go to the [[http://watcut.uwaterloo.ca/cgi-bin/makemultimer/ MakeMultimer Server]], and submit the [[PDB code]] '''1sva'''. | *'''Generate The Capsid''': Go to the [[http://watcut.uwaterloo.ca/cgi-bin/makemultimer/ MakeMultimer Server]], and submit the [[PDB code]] '''1sva'''. | ||
