Re: [PyMOL] mmView - a tool for mmCIF exploration

[Daniel S. <dan...@vs...>]

Hi Troels,

mmView is intended as a web-based viewer (and nothing more) of the
textual mmCIF format, which i used by the PDB database as its archival
format. mmCIF offers, with its flexible syntax, much better solution
for storing biomolecular structures than the PDB format. However,
mmCIF format is primarily intended for automatic processing, and is
thus, in contrary to PDB format, much less readable by human.

The data in the mmCIF format are stored as database tables (called
categories), and our tool tries to facilitate the work with mmCIF
files. All data shown by mmView are taken from the mmCIF file with the
only exception, which is the abstract of the structure citation that
is downloaded automatically from Pubmed database.

Sure there is overlap with Proteopedia, however Proteopedia's aim is
apparently to provide as much information about the given structure as
possible (and there is much much more information in Proteopedia than
in mmView, and certainly some information in Proteopedia is obtained
from the mmCIF or PDB file). The aim of mmView is to present mmCIF
categories in more readable form, and in addition some information
about the structure we regard as interesting is aggregated from more
categorie and presented in a summary form.

We use mmView in the classes of structural biology and structural
bioinformatics, and our experience shows that students grasp much
easily basic principles of the mmCIF format if it is presented this
way.

More information about mmView you can find in the BMC Rasearch Notes
journal: http://www.biomedcentral.com/content/pdf/1756-0500-4-121.pdf.

Regards
  Daniel

2011/12/6 Troels Emtekær Linnet <tl...@gm...>:
> That reminds me of:
>
> http://www.proteopedia.org/wiki/index.php/4ins
>
> What is the difference between the two web pages?
>
> Best
> Troels
>
>
> 2011/12/6 Daniel Svozil <dan...@vs...<mailto:dan...@vs...>>
> Dear colleagues,
>
> We would like to announce the availability of mmView - the web-based
> application which allows to comfortably explore the structural data of
> biomacromolecules stored in the mmCIF (macromolecular Crystallographic
> Information File) format. The mmView software system is primarily
> intended for educational purposes but it can also serve as an
> auxiliary tool for working with biomolecular structures.
>
> The mmView application is offered in two flavors: as a publicly
> available web server http://ich.vscht.cz/projects/mmview/, and as an
> open-source stand-alone application (available from
> http://sourceforge.net/projects/mmview) that can be installed on the
> user’s computer.
>
> Petr Cech and Daniel Svozil
>
> --
> Daniel Svozil, PhD
> Head of Laboratory of Informatics and Chemistry
> Institute of Chemical Technology
> Czech Republic
>
> phone: +420 220 444 391<tel:%2B420%20220%20444%20391>
> http://ich.vscht.cz/~svozil
>
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-- 
Daniel Svozil, PhD
Head of Laboratory of Informatics and Chemistry
Institute of Chemical Technology
Czech Republic

phone: +420 220 444 391
http://ich.vscht.cz/~svozil