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CMView specifications

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Unique identifier OMICS_07132
Name CMView
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Version 1.1
Stability Stable
Maintained Yes

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Publication for CMView

CMView in pipeline

2016
PMCID: 4797681
PMID: 27053964
DOI: 10.2174/1874091X01610010001

[…] do md simulations. at the moment puma has been chosen for md modeling [,]. occasionally it is also required to use other programs (for example hyperchem) for preparing md structure., in contrast to cmview, the tamd program is designed mainly to analyze md trajectories. tamd provides an adjustable output of molecular animation (without running external programs such as pymol []) […]


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CMView in publications

 (7)
PMCID: 4797681
PMID: 27053964
DOI: 10.2174/1874091X01610010001

[…] a useful approach of representation of structural data helping researcher in determination of structural properties such as domain architecture, secondary structure and contacts between clusters. cmview [,] combines rich possibilities of contact maps analysis with 3d visualization using pymol. it provides functions for calculation of a contact map from the 3d structure, basic editing, 3d […]

PMCID: 4388261
PMID: 25849385
DOI: 10.1107/S1399004715000292

[…] shown in figs. 2 and 4 were generated using the modevector.py script from the pymolwiki website (http://www.pymolwiki.org) with a 0.5 å cutoff, and the difference-distance maps were calculated using cmview (vehlow et al., 2011). the internal cavities in figs. 11 and 12 were generated using the hollow tool (ho & gruswitz, 2008). finally, the secondary-structure assignments of hewl used […]

PMCID: 4005737
PMID: 24788065
DOI: 10.1371/journal.pone.0095183

[…] interactions between regions or differences between the clades. a 10 å cut-off distance between the c-alpha carbons was considered as a measure for contact . contact maps were generated with cmview v0.9.6, after loading the appropriate molecular structure by specifying its pdb identification number. the software allows to highlight relevant regions (e.g. c3 or c4 of env) or single […]

PMCID: 3839912
PMID: 24282583
DOI: 10.1371/journal.pone.0081346

[…] quantitative information about the stability of the models (root mean square deviation; rmsd) and to determine the flexible regions of the structures (b factor). the structures were analyzed with cmview program version 1.1 []. the amino acid accessibilities were calculated with naccess program version 2.1.1 [] that use the lee and richards method []., this work has benefited […]

PMCID: 3633016
PMID: 23815292
DOI: 10.1186/1471-2105-14-S7-S13

[…] this is due to the fact that the graphs are protein backbones., proteins contact maps dataset pdbsv3 dataset contains 50 contact maps of the amino acids of the domains of the proteins, retrieved by cmview []. while for backbones we can have thousands of vertices corresponding to atoms, the number of vertices in the contact maps is relatively small (corresponds to the length of the proteins), […]


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CMView institution(s)
Department of Simulations and Graphics, OvG University Magdeburg, Berlin, Germany

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