This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
Sandbox1rpu
From Proteopedia
(New page: This works: {{Structure |PDB= 1rpu |SIZE=400|SCENE=User:Wayne_Decatur/Plant_Viral_Protein_p19_Suppression_of_RNA_Silencing/Molecular_caliper_surface/2|CAPTION= okay but I need wireframes f...) |
m (try adding 1d66 to get SAT to show up) |
||
| (16 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | This works: | + | configuration&isosurfaces&dots for p19 tour problematic until did one step at a time using console |
| + | |||
| + | <Structure load='1d66' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /> | ||
| + | |||
| + | ==This works:== | ||
{{Structure | {{Structure | ||
| - | |PDB= 1rpu |SIZE=400|SCENE= | + | |PDB= 1rpu |SIZE=400|SCENE=Sandbox1rpu/Molecular_caliper/1|CAPTION= okay but I need wireframes for some other views |
|SITE= | |SITE= | ||
|LIGAND= | |LIGAND= | ||
| Line 11: | Line 15: | ||
}} | }} | ||
| - | + | ||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | ==this works now too and I made it using view above and configuration 1 and rebuilding one line at a time in jmol console:== | ||
{{Structure | {{Structure | ||
| - | |PDB= 1rpu |SIZE=400|SCENE= | + | |PDB= 1rpu |SIZE=400|SCENE=Sandbox1rpu/Molecular_caliper_prefected/2|CAPTION= 1rpu, resolution 2.50Å (<scene name='Sandbox1rpu/Molecular_caliper_prefected/2'>initial scene</scene>) |
|SITE= | |SITE= | ||
|LIGAND= | |LIGAND= | ||
| Line 22: | Line 65: | ||
|RESOURCES=<span class='plainlinks'><!--[http://www-unix.oit.umass.edu/~wdecatur/p19tutorial/ Explorable Tour], Eric Martz felt no one would look here-->[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rpu OCA], [http://www.ebi.ac.uk/pdbsum/1rpu PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rpu RCSB]</span> | |RESOURCES=<span class='plainlinks'><!--[http://www-unix.oit.umass.edu/~wdecatur/p19tutorial/ Explorable Tour], Eric Martz felt no one would look here-->[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rpu OCA], [http://www.ebi.ac.uk/pdbsum/1rpu PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rpu RCSB]</span> | ||
}} | }} | ||
| + | |||
| + | |||
| + | WEIRD thing with configuration I saw on October 24th 2009. When I enter 'configuration 1;' or 'configuration 2;' console in Proteopedia SAT, then it added weird lines from bases and among protein that were faint but I couldn't get rid of. It wouldn't happen in the newest version of FirstGlance linked to 1rpu page but then later it even wouldn't happen in SAT when I initiated new browser windows and JAVA runs. At first I thought it was leaving off the semi-colon but then it seemed to work with the semi-colon everywhere too. So another weird thing like when you need to scroll side of browser window to get a stuck animation going. | ||
Current revision
configuration&isosurfaces&dots for p19 tour problematic until did one step at a time using console
|
This works:
| |||||||
| okay but I need wireframes for some other views | |||||||
|---|---|---|---|---|---|---|---|
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
this works now too and I made it using view above and configuration 1 and rebuilding one line at a time in jmol console:
| |||||||
| 1rpu, resolution 2.50Å () | |||||||
|---|---|---|---|---|---|---|---|
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
WEIRD thing with configuration I saw on October 24th 2009. When I enter 'configuration 1;' or 'configuration 2;' console in Proteopedia SAT, then it added weird lines from bases and among protein that were faint but I couldn't get rid of. It wouldn't happen in the newest version of FirstGlance linked to 1rpu page but then later it even wouldn't happen in SAT when I initiated new browser windows and JAVA runs. At first I thought it was leaving off the semi-colon but then it seemed to work with the semi-colon everywhere too. So another weird thing like when you need to scroll side of browser window to get a stuck animation going.
