Re: [Jmol-users] delay DOCUMENTATION

2011-12-07 Thread Robert Hanson 
Thanks -- done!

On Wed, Dec 7, 2011 at 11:37 AM, Eric Martz wrote:

> Dear Bob,
>
> Under "delay", please include "set delayMaximumMs" under See also. Thanks!
>
> -Eric
>
>
>
> --
> Cloud Services Checklist: Pricing and Packaging Optimization
> This white paper is intended to serve as a reference, checklist and point
> of
> discussion for anyone considering optimizing the pricing and packaging
> model
> of a cloud services business. Read Now!
> http://www.accelacomm.com/jaw/sfnl/114/51491232/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Cloud Services Checklist: Pricing and Packaging Optimization
This white paper is intended to serve as a reference, checklist and point of 
discussion for anyone considering optimizing the pricing and packaging model 
of a cloud services business. Read Now!
http://www.accelacomm.com/jaw/sfnl/114/51491232/___
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Re: [Jmol-users] mmView - a tool for mmCIF exploration

2011-12-07 Thread Robert Hanson 
On Wed, Dec 7, 2011 at 12:57 PM, Daniel Svozil wrote:

> Dear Bob,
>
> thanks for your complimment! I can't edit Jmol's wiki, as Wiki does
> not send me a message to confirm my e-mail address (I was waiting for
> e-mail the whole day, that's why my response is delayed), and if my
> address is not authenticated I don't have permissions to change any
> wiki page. I didn't find any contact where I could report this
> problem.
>
> Regarding crystal contacts, mmView is primarily aimed as web-based
> viewer of the mmCIF format. All data shown in the application are
> taken from the mmCIF file (with the only exception of paper abstracts
> that are downloaded of the Pubmed). mmCIF does not store any
> information about crystal contacts, these would have to be calculated.
> Implementation of the functionality going beyond simple display of the
> mmCIF data is not on our todo list, however, we may add some
> analytical tools in the future. And thus we welcome any suggestions
> from the community.
>
>
Exactly my point. The Jmol applet you have there can calculate and
visualize those contacts as well as show the unit cell, symmetry-related
duplication within the cell, etc.

(As well as extract out of the CIF file any information whatsoever that is
in there, but that's another point unrelated to this one. You have decided
to do that on your server, so that's not something you would need Jmol to
do, I guess.)

Please let me know if you are interested in exploring that.

Bob







> Daniel
>
> On Tue, Dec 6, 2011 at 2:13 PM, Robert Hanson  wrote:
> > Very nice! Congratulations. Please to get your page added to
> http://wiki.jmol.org/index.php/Websites_Using_Jmol
> >
> > Suggestions: I would think the MMCIF crowd might be interested in seeing
> the results of crystal packing and contacts. Any thoughts on that?
> >
> > Bob Hanson
> >
> >
> > On Tue, Dec 6, 2011 at 5:36 AM, Daniel Svozil  > wrote:
> > 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
> > http://ich.vscht.cz/~svozil
> >
> >
> --
> > Cloud Services Checklist: Pricing and Packaging Optimization
> > This white paper is intended to serve as a reference, checklist and
> point of
> > discussion for anyone considering optimizing the pricing and packaging
> model
> > of a cloud services business. Read Now!
> > http://www.accelacomm.com/jaw/sfnl/114/51491232/
> > ___
> > Jmol-users mailing list
> > Jmol-users@lists.sourceforge.net >
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
> >
> >
> > --
> > Robert M. Hanson
> > Professor of Chemistry
> > St. Olaf College
> > 1520 St. Olaf Ave.
> > Northfield, MN 55057
> > http://www.stolaf.edu/people/hansonr
> > phone: 507-786-3107
> >
> >
> > If nature does not answer first what we want,
> > it is better to take what answer we get.
> >
> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
> --
> 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
>
>
> --
> Cloud Services Checklist: Pricing and Packaging Optimization
> This white paper is intended to serve as a reference, checklist and point
> of
> discussion for anyone considering optimizing the pricing and packaging
> model
> of a cloud services business. Read Now!
> http://www.accelacomm.com/jaw/sfnl/114/51491232/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah W

Re: [Jmol-users] mmView - a tool for mmCIF exploration

2011-12-07 Thread Daniel Svozil 
Dear Angel,

it would be nice if you can add the following link:

mmView (http://ich.vscht.cz/projects/mmview/) Lab. of Informatics and
Chemistry, ICT Prague, Czech Republic. Web-based viewer of the the
mmCIF files.

Thanks a lot!

Daniel

2011/12/7 Angel Herráez :
> Hello Daniel
>
> Yes, we have had another rreport of the confirmation email not arriving.
> Aministration of the wiki is done by Nico, who lacks time for this lately. 
> The problem will be
> looked at as soon as possible.
> Reporting here is enough. I will remind Nico about this problem. Meanwhile, I 
> can add the link
> if you want. Please, provide the text and URL you would like to insert.
>
> Regards
> Angel
>
>
>
> --
> Cloud Services Checklist: Pricing and Packaging Optimization
> This white paper is intended to serve as a reference, checklist and point of
> discussion for anyone considering optimizing the pricing and packaging model
> of a cloud services business. Read Now!
> http://www.accelacomm.com/jaw/sfnl/114/51491232/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users



-- 
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

--
Cloud Services Checklist: Pricing and Packaging Optimization
This white paper is intended to serve as a reference, checklist and point of 
discussion for anyone considering optimizing the pricing and packaging model 
of a cloud services business. Read Now!
http://www.accelacomm.com/jaw/sfnl/114/51491232/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] mmView - a tool for mmCIF exploration

2011-12-07 Thread Angel Herráez 
Hello Daniel

Yes, we have had another rreport of the confirmation email not arriving.
Aministration of the wiki is done by Nico, who lacks time for this lately. The 
problem will be 
looked at as soon as possible.
Reporting here is enough. I will remind Nico about this problem. Meanwhile, I 
can add the link 
if you want. Please, provide the text and URL you would like to insert.

Regards
Angel



--
Cloud Services Checklist: Pricing and Packaging Optimization
This white paper is intended to serve as a reference, checklist and point of 
discussion for anyone considering optimizing the pricing and packaging model 
of a cloud services business. Read Now!
http://www.accelacomm.com/jaw/sfnl/114/51491232/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] mmView - a tool for mmCIF exploration

2011-12-07 Thread Daniel Svozil 
Dear Bob,

thanks for your complimment! I can't edit Jmol's wiki, as Wiki does
not send me a message to confirm my e-mail address (I was waiting for
e-mail the whole day, that's why my response is delayed), and if my
address is not authenticated I don't have permissions to change any
wiki page. I didn't find any contact where I could report this
problem.

Regarding crystal contacts, mmView is primarily aimed as web-based
viewer of the mmCIF format. All data shown in the application are
taken from the mmCIF file (with the only exception of paper abstracts
that are downloaded of the Pubmed). mmCIF does not store any
information about crystal contacts, these would have to be calculated.
Implementation of the functionality going beyond simple display of the
mmCIF data is not on our todo list, however, we may add some
analytical tools in the future. And thus we welcome any suggestions
from the community.

Daniel

On Tue, Dec 6, 2011 at 2:13 PM, Robert Hanson  wrote:
> Very nice! Congratulations. Please to get your page added to 
> http://wiki.jmol.org/index.php/Websites_Using_Jmol
>
> Suggestions: I would think the MMCIF crowd might be interested in seeing the 
> results of crystal packing and contacts. Any thoughts on that?
>
> Bob Hanson
>
>
> On Tue, Dec 6, 2011 at 5:36 AM, Daniel Svozil 
> mailto:daniel.svo...@vscht.cz>> wrote:
> 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
> http://ich.vscht.cz/~svozil
>
> --
> Cloud Services Checklist: Pricing and Packaging Optimization
> This white paper is intended to serve as a reference, checklist and point of
> discussion for anyone considering optimizing the pricing and packaging model
> of a cloud services business. Read Now!
> http://www.accelacomm.com/jaw/sfnl/114/51491232/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900



-- 
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

--
Cloud Services Checklist: Pricing and Packaging Optimization
This white paper is intended to serve as a reference, checklist and point of 
discussion for anyone considering optimizing the pricing and packaging model 
of a cloud services business. Read Now!
http://www.accelacomm.com/jaw/sfnl/114/51491232/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] delay DOCUMENTATION

2011-12-07 Thread Eric Martz 
Dear Bob,

Under "delay", please include "set delayMaximumMs" under See also. Thanks!

-Eric


--
Cloud Services Checklist: Pricing and Packaging Optimization
This white paper is intended to serve as a reference, checklist and point of 
discussion for anyone considering optimizing the pricing and packaging model 
of a cloud services business. Read Now!
http://www.accelacomm.com/jaw/sfnl/114/51491232/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users