LiteMol:Functionality - Revision history

Matthew: /* Classic features */ mjc

2017-05-05T12:18:21Z

Classic features: mjc

← Older revision		Revision as of 12:18, 5 May 2017
Line 3:		Line 3:
	=Classic features=		=Classic features=
	* Supports all major structural data formats ([http://mmcif.wwpdb.org/ PDBx/mmcif], [https://www.wwpdb.org/documentation/file-format PDB], [http://pubs.acs.org/doi/pdf/10.1021/ci00007a012 SDF]).		* Supports all major structural data formats ([http://mmcif.wwpdb.org/ PDBx/mmcif], [https://www.wwpdb.org/documentation/file-format PDB], [http://pubs.acs.org/doi/pdf/10.1021/ci00007a012 SDF]).
	* All common visualization models ('balls-n-sticks'/cartoon/Cα-trace/VDW spheres/surfaces).		* All common visualization models ('balls-and-sticks'/cartoon/Cα-trace/VDW spheres/surfaces).
	* Displays electron densities for X-ray crystallographic structures and ~~electric~~ potential maps for cryo-EM models.		* Displays electron densities for X-ray crystallographic structures and electronic potential maps for cryo-EM models.
	* Available as a [https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/ standalone viewer] or as a [https://github.com/dsehnal/LiteMol library} for embedding into third party applications.		* Available as a [https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/ standalone viewer] or as a [https://github.com/dsehnal/LiteMol library} for embedding into third party applications.

Matthew: /* Advanced features */ edited mjc

2017-05-04T20:51:58Z

Advanced features: edited mjc

← Older revision		Revision as of 20:51, 4 May 2017
Line 11:		Line 11:

	=Advanced features=		=Advanced features=
	* Introduces the [https://github.com/dsehnal/BinaryCIF BinaryCIF] a compression format compatible with standard PDBx/mmCIF format ''greatly reducing'' amount of transferred data.		* Introduces the [https://github.com/dsehnal/BinaryCIF BinaryCIF] a compression format compatible with standard PDBx/mmCIF format ''greatly reducing'' the amount of transferred data.
	* [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] allows for streaming only parts of the ~~structure models~~ relevant for user ~~deemed~~ visualization. This further ''decreases'' the amount of ''transferred data'' and facilitates ''near instant responsiveness'' even for huge structures ~~like~~ ribosomes and viral capsids. All in your web browser.		* [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] allows for streaming only those parts of the structural model relevant for the user required visualization. This further ''decreases'' the amount of ''transferred data'' and facilitates ''near instant responsiveness'' even for huge structures such as ribosomes and viral capsids. All in your web browser.
	* [http://webchem.ncbr.muni.cz/DensityServer DensityServer ] allows ''instant access'' to full resolution user ~~deemed~~ slices of ''electron density'' (e.g. binding sites) and down sampled surface of the entire biomacromolecular structure.		* [http://webchem.ncbr.muni.cz/DensityServer DensityServer ] allows ''instant access'' to full resolution user determined slices of ''electron density'' (e.g. binding sites) and down sampled surface of the entire biomacromolecular structure.
	* Displays [https://www.wwpdb.org/validation/validation-reports ~~PDB~~ validation reports] and [[ValidatorDB:UserManual \| ValidatorDB ligand validation]].		* Displays [https://www.wwpdb.org/validation/validation-reports wwPDB validation reports] and [[ValidatorDB:UserManual \| ValidatorDB ligand validation]].
	* Displays ''sequence annotations'' from [http://pfam.xfam.org/ Pfam], [https://www.ebi.ac.uk/interpro/ InterPro], [www.cathdb.info CATH], [http://scop.berkeley.edu/ SCOP], [http://www.uniprot.org/ UniProt].		* Displays ''sequence annotations'' from [http://pfam.xfam.org/ Pfam], [https://www.ebi.ac.uk/interpro/ InterPro], [www.cathdb.info CATH], [http://scop.berkeley.edu/ SCOP], [http://www.uniprot.org/ UniProt].
	* Visualizer ~~which~~ requires only an up to date ''web browser'' with no dependencies ~~needed~~. Runs on all ''mobile devices''.		* Visualizer requires only an up-to-date ''web browser'' with no dependencies required. Runs on all ''mobile devices''.
	* Minimal ''memory footprint''.		* Minimal ''memory footprint''.


	[[Image:LiteMol-Performance.png\|center\|800px]]		[[Image:LiteMol-Performance.png\|center\|800px]]

Matthew: edited by MJC

2017-05-04T20:47:54Z

edited by MJC

← Older revision		Revision as of 20:47, 4 May 2017
Line 4:		Line 4:
	* Supports all major structural data formats ([http://mmcif.wwpdb.org/ PDBx/mmcif], [https://www.wwpdb.org/documentation/file-format PDB], [http://pubs.acs.org/doi/pdf/10.1021/ci00007a012 SDF]).		* Supports all major structural data formats ([http://mmcif.wwpdb.org/ PDBx/mmcif], [https://www.wwpdb.org/documentation/file-format PDB], [http://pubs.acs.org/doi/pdf/10.1021/ci00007a012 SDF]).
	* All common visualization models ('balls-n-sticks'/cartoon/Cα-trace/VDW spheres/surfaces).		* All common visualization models ('balls-n-sticks'/cartoon/Cα-trace/VDW spheres/surfaces).
	* Displays x-ray ~~electron densities~~ and electric potential cryo-EM ~~maps~~.		* Displays electron densities for X-ray crystallographic structures and electric potential maps for cryo-EM models.
	* Available as a [https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/ standalone viewer] or as a [https://github.com/dsehnal/LiteMol library} for embedding into third party applications.		* Available as a [https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/ standalone viewer] or as a [https://github.com/dsehnal/LiteMol library} for embedding into third party applications.

Lukas at 12:05, 19 April 2017

2017-04-19T12:05:20Z

← Older revision		Revision as of 12:05, 19 April 2017
Line 5:		Line 5:
	* All common visualization models ('balls-n-sticks'/cartoon/Cα-trace/VDW spheres/surfaces).		* All common visualization models ('balls-n-sticks'/cartoon/Cα-trace/VDW spheres/surfaces).
	* Displays x-ray electron densities and electric potential cryo-EM maps.		* Displays x-ray electron densities and electric potential cryo-EM maps.
	* Available as a standalone viewer or as a library for embedding into third party applications.		* Available as a [https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/ standalone viewer] or as a [https://github.com/dsehnal/LiteMol library} for embedding into third party applications.


Line 13:		Line 13:
	* Introduces the [https://github.com/dsehnal/BinaryCIF BinaryCIF] a compression format compatible with standard PDBx/mmCIF format ''greatly reducing'' amount of transferred data.		* Introduces the [https://github.com/dsehnal/BinaryCIF BinaryCIF] a compression format compatible with standard PDBx/mmCIF format ''greatly reducing'' amount of transferred data.
	* [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] allows for streaming only parts of the structure models relevant for user deemed visualization. This further ''decreases'' the amount of ''transferred data'' and facilitates ''near instant responsiveness'' even for huge structures like ribosomes and viral capsids. All in your web browser.		* [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] allows for streaming only parts of the structure models relevant for user deemed visualization. This further ''decreases'' the amount of ''transferred data'' and facilitates ''near instant responsiveness'' even for huge structures like ribosomes and viral capsids. All in your web browser.
	* [http://webchem.ncbr.muni.cz/DensityServer DensityServer ] - allows ''instant access'' to full resolution slices of ''electron density'' (e.g. binding sites) and down sampled surface of the entire ~~macromolecular~~ structure.		* [http://webchem.ncbr.muni.cz/DensityServer DensityServer ] allows ''instant access'' to full resolution user deemed slices of ''electron density'' (e.g. binding sites) and down sampled surface of the entire biomacromolecular structure.
	* Displays [https://www.wwpdb.org/validation/validation-reports PDB validation reports] and [[ValidatorDB:UserManual \| ValidatorDB ligand validation]].		* Displays [https://www.wwpdb.org/validation/validation-reports PDB validation reports] and [[ValidatorDB:UserManual \| ValidatorDB ligand validation]].
	* Displays ''sequence annotations'' from [http://pfam.xfam.org/ Pfam], [https://www.ebi.ac.uk/interpro/ InterPro], [www.cathdb.info CATH}, [http://scop.berkeley.edu/ SCOP], [http://www.uniprot.org/ UniProt].		* Displays ''sequence annotations'' from [http://pfam.xfam.org/ Pfam], [https://www.ebi.ac.uk/interpro/ InterPro], [www.cathdb.info CATH], [http://scop.berkeley.edu/ SCOP], [http://www.uniprot.org/ UniProt].
	* ~~The only visualizer~~ which requires only an up to date ''web browser'' with no dependencies needed. Runs on all ''mobile devices''.		* Visualizer which requires only an up to date ''web browser'' with no dependencies needed. Runs on all ''mobile devices''.
	* Minimal ''memory footprint''.		* Minimal ''memory footprint''.


	[[Image:LiteMol-Performance.png\|center\|800px]]		[[Image:LiteMol-Performance.png\|center\|800px]]

Lukas: /* Advanced Features */

2017-04-10T13:59:05Z

Advanced Features

← Older revision		Revision as of 13:59, 10 April 2017
Line 10:		Line 10:
	[[Image:LiteMol-Models.png\|center\|800px]]		[[Image:LiteMol-Models.png\|center\|800px]]

	=Advanced ~~Features~~=		=Advanced features=
	* Introduces the [https://github.com/dsehnal/BinaryCIF BinaryCIF] a compression format compatible with standard PDBx/mmCIF format ''greatly reducing'' amount of transferred data.		* Introduces the [https://github.com/dsehnal/BinaryCIF BinaryCIF] a compression format compatible with standard PDBx/mmCIF format ''greatly reducing'' amount of transferred data.
	* [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] allows for streaming only parts of the structure models relevant for user deemed visualization. This further ''decreases'' the amount of ''transferred data'' and facilitates ''near instant responsiveness'' even for huge structures like ribosomes and viral capsids. All in your web browser.		* [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] allows for streaming only parts of the structure models relevant for user deemed visualization. This further ''decreases'' the amount of ''transferred data'' and facilitates ''near instant responsiveness'' even for huge structures like ribosomes and viral capsids. All in your web browser.

Lukas: /* Classic Features */

2017-04-10T13:58:53Z

Classic Features

← Older revision		Revision as of 13:58, 10 April 2017
Line 1:		Line 1:
	{{large\| '''LiteMol is a powerful and blazing-fast cross-platform tool for handling 3D macromolecular data in the browser. [https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/ Try it now!]'''}}		{{large\| '''LiteMol is a powerful and blazing-fast cross-platform tool for handling 3D macromolecular data in the browser. [https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/ Try it now!]'''}}

	=Classic ~~Features~~=		=Classic features=
	* Supports all major structural data formats ([http://mmcif.wwpdb.org/ PDBx/mmcif], [https://www.wwpdb.org/documentation/file-format PDB], [http://pubs.acs.org/doi/pdf/10.1021/ci00007a012 SDF]).		* Supports all major structural data formats ([http://mmcif.wwpdb.org/ PDBx/mmcif], [https://www.wwpdb.org/documentation/file-format PDB], [http://pubs.acs.org/doi/pdf/10.1021/ci00007a012 SDF]).
	* All common visualization models ('balls-n-sticks'/cartoon/Cα-trace/VDW spheres/surfaces).		* All common visualization models ('balls-n-sticks'/cartoon/Cα-trace/VDW spheres/surfaces).

Lukas: /* Advanced Features */

2017-04-10T13:39:25Z

Advanced Features

← Older revision		Revision as of 13:39, 10 April 2017
Line 11:		Line 11:

	=Advanced Features=		=Advanced Features=
	* Introduces the [https://github.com/dsehnal/BinaryCIF BinaryCIF] a compression format compatible with standard PDBx/mmCIF format greatly reducing amount of transferred data.		* Introduces the [https://github.com/dsehnal/BinaryCIF BinaryCIF] a compression format compatible with standard PDBx/mmCIF format ''greatly reducing'' amount of transferred data.
	* [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] allows for streaming only parts of the structure models relevant for user deemed visualization. This further decreases the amount of transferred data and facilitates near instant responsiveness even for huge structures like ribosomes and viral capsids. All in your web browser.		* [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] allows for streaming only parts of the structure models relevant for user deemed visualization. This further ''decreases'' the amount of ''transferred data'' and facilitates ''near instant responsiveness'' even for huge structures like ribosomes and viral capsids. All in your web browser.
	* [http://webchem.ncbr.muni.cz/DensityServer DensityServer ] - allows instant access to full ~~resulution~~ slices of electron density (e.g. binding sites) and ~~downsampled~~ surface of the entire macromolecular structure.		* [http://webchem.ncbr.muni.cz/DensityServer DensityServer ] - allows ''instant access'' to full resolution slices of ''electron density'' (e.g. binding sites) and down sampled surface of the entire macromolecular structure.
	* The only visualizer which requires only an up to date web browser with no dependencies needed. Runs on all mobile devices.		* Displays [https://www.wwpdb.org/validation/validation-reports PDB validation reports] and [[ValidatorDB:UserManual \| ValidatorDB ligand validation]].
	* Minimal memory footprint.		* Displays ''sequence annotations'' from [http://pfam.xfam.org/ Pfam], [https://www.ebi.ac.uk/interpro/ InterPro], [www.cathdb.info CATH}, [http://scop.berkeley.edu/ SCOP], [http://www.uniprot.org/ UniProt].
			* The only visualizer which requires only an up to date ''web browser'' with no dependencies needed. Runs on all ''mobile devices''.
			* Minimal ''memory footprint''.


	[[Image:LiteMol-Performance.png\|center\|800px]]		[[Image:LiteMol-Performance.png\|center\|800px]]

Lukas: /* Classic Features */

2017-04-10T13:25:15Z

Classic Features

← Older revision		Revision as of 13:25, 10 April 2017
Line 4:		Line 4:
	* Supports all major structural data formats ([http://mmcif.wwpdb.org/ PDBx/mmcif], [https://www.wwpdb.org/documentation/file-format PDB], [http://pubs.acs.org/doi/pdf/10.1021/ci00007a012 SDF]).		* Supports all major structural data formats ([http://mmcif.wwpdb.org/ PDBx/mmcif], [https://www.wwpdb.org/documentation/file-format PDB], [http://pubs.acs.org/doi/pdf/10.1021/ci00007a012 SDF]).
	* All common visualization models ('balls-n-sticks'/cartoon/Cα-trace/VDW spheres/surfaces).		* All common visualization models ('balls-n-sticks'/cartoon/Cα-trace/VDW spheres/surfaces).
			* Displays x-ray electron densities and electric potential cryo-EM maps.
	* Available as a standalone viewer or as a library for embedding into third party applications.		* Available as a standalone viewer or as a library for embedding into third party applications.
	* Displays x-ray electron densities and electric potential cryo-EM maps.

Lukas: /* Classic Features */

2017-04-10T13:23:52Z

Classic Features

← Older revision		Revision as of 13:23, 10 April 2017
Line 3:		Line 3:
	=Classic Features=		=Classic Features=
	* Supports all major structural data formats ([http://mmcif.wwpdb.org/ PDBx/mmcif], [https://www.wwpdb.org/documentation/file-format PDB], [http://pubs.acs.org/doi/pdf/10.1021/ci00007a012 SDF]).		* Supports all major structural data formats ([http://mmcif.wwpdb.org/ PDBx/mmcif], [https://www.wwpdb.org/documentation/file-format PDB], [http://pubs.acs.org/doi/pdf/10.1021/ci00007a012 SDF]).
	* All common visualization models ('balls-n-sticks'/cartoon/Cα-~~trance~~/VDW spheres/surfaces).		* All common visualization models ('balls-n-sticks'/cartoon/Cα-trace/VDW spheres/surfaces).
	* Available as a standalone viewer or as a library for embedding into third party applications.		* Available as a standalone viewer or as a library for embedding into third party applications.
	* Displays x-ray electron densities and electric potential cryo-EM maps.		* Displays x-ray electron densities and electric potential cryo-EM maps.

Lukas: Initiall commit

2017-04-10T13:23:03Z

Initiall commit

New page

{{large| '''LiteMol is a powerful and blazing-fast cross-platform tool for handling 3D macromolecular data in the browser. [https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/ Try it now!]'''}}

=Classic Features=
* Supports all major structural data formats ([http://mmcif.wwpdb.org/ PDBx/mmcif], [https://www.wwpdb.org/documentation/file-format PDB], [http://pubs.acs.org/doi/pdf/10.1021/ci00007a012 SDF]).
* All common visualization models ('balls-n-sticks'/cartoon/Cα-trance/VDW spheres/surfaces).
* Available as a standalone viewer or as a library for embedding into third party applications.
* Displays x-ray electron densities and electric potential cryo-EM maps.

[[Image:LiteMol-Models.png|center|800px]]

=Advanced Features=
* Introduces the [https://github.com/dsehnal/BinaryCIF BinaryCIF] a compression format compatible with standard PDBx/mmCIF format greatly reducing amount of transferred data.
* [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] allows for streaming only parts of the structure models relevant for user deemed visualization. This further decreases the amount of transferred data and facilitates near instant responsiveness even for huge structures like ribosomes and viral capsids. All in your web browser.
* [http://webchem.ncbr.muni.cz/DensityServer DensityServer ] - allows instant access to full resulution slices of electron density (e.g. binding sites) and downsampled surface of the entire macromolecular structure.
* The only visualizer which requires only an up to date web browser with no dependencies needed. Runs on all mobile devices.
* Minimal memory footprint.

[[Image:LiteMol-Performance.png|center|800px]]