Jmol/Visualizing large molecules: Difference between revisions

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Eric Martz (talk | contribs)
ConfirmAccount, Editor, Print3D, Tester, journal, Administrators
30,118 edits
Eric Martz (talk | contribs)
ConfirmAccount, Editor, Print3D, Tester, journal, Administrators
30,118 edits
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====SV40 Capsid Alpha Carbons====
====SV40 Capsid Alpha Carbons====


*'''Get the Address of the Capsid Structure''': Go to [http://viperdb.scripps.edu ViperDB], and submit the [[PDB code]] '''1sva'''.
*'''Run the Jmol Application''' in a working folder. [[Jmol/Application|Here are '''instructions'''.]]


*'''Free Java Memory''': You will need all of your default java memory, so first you should close any java-based programs. Close all browser windows or tabs that contain the Jmol applet. Close the Jmol application.
*'''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''': After MakeMultimer displays the results page, right-click on the link '''1sva_mm1.pdb''', and copy the link location. It will be something like <nowiki>http://watcut.uwaterloo.ca/mm_static/tmpA-_B8L/1sva_mm1.pdb</nowiki>, but this address is temporary and later the file will be deleted from the server. In the Jmol application (see above for instructions), enter this command
*'''Display The Alpha Carbons''': In the Jmol application, enter this command
:<tt>load <nowiki>http://watcut.uwaterloo.ca/mm_static/tmpA-_B8L/1sva_mm1.pdb</nowiki> filter "*.ca"
:<tt>load <nowiki>http://viperdb.scripps.edu/OLIGOMERS/1sva_full.vdb.gz</nowiki> filter "*.ca"
 
viperdb.scripps.edu
http://viperdb.scripps.edu/OLIGOMERS/1sva_full.vdb.gz
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