Jmol/Visualizing large molecules: Difference between revisions
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*'''Get the Address of the Capsid Structure''': Go to [http://viperdb.scripps.edu ViperDB], and submit the [[PDB code]] '''1sva'''. Right click on the link ''full capsid'', then ''copy link location''. For 1sva, it is <nowiki>http://viperdb.scripps.edu/OLIGOMERS/1sva_full.vdb.gz</nowiki>. | *'''Get the Address of the Capsid Structure''': Go to [http://viperdb.scripps.edu ViperDB], and submit the [[PDB code]] '''1sva'''. Right click on the link ''full capsid'', then ''copy link location''. For 1sva, it is <nowiki>http://viperdb.scripps.edu/OLIGOMERS/1sva_full.vdb.gz</nowiki>. | ||
*'''Display The Alpha Carbons''': In the Jmol application, enter | *'''Display The Alpha Carbons''': In the Jmol application, enter these commands | ||
:<tt>load <nowiki>http://viperdb.scripps.edu/OLIGOMERS/1sva_full.vdb.gz</nowiki> filter "*.ca" | :<tt>load <nowiki>http://viperdb.scripps.edu/OLIGOMERS/1sva_full.vdb.gz</nowiki> filter "*.ca" | ||
:color chain</tt> | |||
It may take about a minute for the first command to work. After the capsid appears, enter the second command -- it may take half a minute. The resulting display will include 123,420 atoms, which is about the maximum that Jmol can display in the default java memory. | |||
If the SV40 full capsid display fails, try the half-capsid model (also available from a link at ViperDB). | |||
