User:Eric Martz/Sandbox 18: Difference between revisions

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When the original PDB file contains ligand hetero atoms, the script from FirstGlance using JSmol 14.32.64c does not work in JSmol 14.31.8. I think this is because the older version does not load the ligand heteroatoms, while the newer version does. I suspect this causes the atomindices to be different so that the select commands don't work, but I haven't verified that.

When the original PDB file happens to have NO ligand hetero atoms, the FirstGlance script works in the old JSmol. I have experimented with such a case, 6bp8.

FIRST TRY

This scene was saved after dropping into the SAT JSmol a script from FirstGlance modified with this command:

<pre>

load "" FILTER "*.CA;biomolecule 1;bmchains;/=3"

</pre>

The scene renders perfectly in the SAT JSmol, rendering 20,358 alpha carbons. But when saved and played back from this green link

<scene name='91/918475/6bp8/1'>Vault eukaryotic nanocompartment</scene>

only the asymmetric unit (6,157 nonH atoms, 782 alpha carbons) loads. This is because the script saved by the SAT has removed the FILTER "..." from the original load command:

[:https://proteopedia.org/wiki/scripts/91/918475/6bp8/1.spt].

</StructureSection>

@@ Line 1: / Line 1: @@
 <StructureSection load='' size='350' side='right' caption='' scene=''>
+When the original PDB file contains ligand hetero atoms, the script from FirstGlance using JSmol 14.32.64c does not work in JSmol 14.31.8. I think this is because the older version does not load the ligand heteroatoms, while the newer version does. I suspect this causes the atomindices to be different so that the select commands don't work, but I haven't verified that.
+When the original PDB file happens to have NO ligand hetero atoms, the FirstGlance script works in the old JSmol. I have experimented with such a case, 6bp8.
+FIRST TRY
+This scene was saved after dropping into the SAT JSmol a script from FirstGlance modified with this command:
+<pre>
+load "" FILTER "*.CA;biomolecule 1;bmchains;/=3"
+</pre>
+The scene renders perfectly in the SAT JSmol, rendering 20,358 alpha carbons. But when saved and played back from this green link
 <scene name='91/918475/6bp8/1'>Vault eukaryotic nanocompartment</scene>
+only the asymmetric unit (6,157 nonH atoms, 782 alpha carbons) loads. This is because the script saved by the SAT has removed the FILTER "..." from the original load command:
+[:https://proteopedia.org/wiki/scripts/91/918475/6bp8/1.spt].
 </StructureSection>