User:Eric Martz/Sandbox 18 - Revision history

Eric Martz at 18:47, 28 July 2022

Eric Martz — Thu, 28 Jul 2022 18:47:44 GMT

←Older revision		Revision as of 18:47, 28 July 2022
Line 12:		Line 12:
	The scene renders perfectly in the SAT JSmol, rendering 20,358 alpha carbons. But when saved and played back from this green link		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>		<scene name='91/918475/6bp8/1'>Vault eukaryotic nanocompartment</scene>
-	only the asymmetric unit (6,157 nonH atoms, 782 alpha carbons) loads. ~~It fails to render, but spacefill shows it. The FILTER in~~ the ~~load command~~ has ~~been ignored. JSmol reports an error with either~~ "~~load . FILTER~~ ..." ~~or "~~load ~~FILTER~~ ...".	+	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>		</StructureSection>

Eric Martz — Thu, 28 Jul 2022 18:43:36 GMT

←Older revision		Revision as of 18:43, 28 July 2022
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	<StructureSection load='' size='350' side='right' caption='' scene=''>		<StructureSection load='' size='350' side='right' caption='' scene=''>

-	When the original PDB file contains ligand hetero atoms, the script from FirstGlance	+	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		FIRST TRY

Eric Martz — Thu, 28 Jul 2022 18:40:49 GMT

←Older revision		Revision as of 18:40, 28 July 2022
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	<StructureSection load='' size='350' side='right' caption='' scene=''>		<StructureSection load='' size='350' side='right' caption='' scene=''>

		+	When the original PDB file contains ligand hetero atoms, the script from FirstGlance
		+
		+	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>		<scene name='91/918475/6bp8/1'>Vault eukaryotic nanocompartment</scene>
		+	only the asymmetric unit (6,157 nonH atoms, 782 alpha carbons) loads. It fails to render, but spacefill shows it. The FILTER in the load command has been ignored. JSmol reports an error with either "load . FILTER ..." or "load FILTER ...".

	</StructureSection>		</StructureSection>

Eric Martz — Thu, 28 Jul 2022 18:25:07 GMT

←Older revision		Revision as of 18:25, 28 July 2022
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-
	<StructureSection load='' size='350' side='right' caption='' scene=''>		<StructureSection load='' size='350' side='right' caption='' scene=''>

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

	</StructureSection>		</StructureSection>

Eric Martz — Thu, 28 Jul 2022 18:22:33 GMT

←Older revision		Revision as of 18:22, 28 July 2022
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-	~~Nothing here yet~~	+
		+	<StructureSection load='' size='350' side='right' caption='' scene=''>
		+
		+	Vault eukaryotic nanocompartment
		+
		+	</StructureSection>

Eric Martz — Thu, 28 Jul 2022 16:19:48 GMT

New page: Nothing here yet

New page

Nothing here yet