Hi, Bob. Thanks for the advice!
The fact is that in our lab we use jmol "as a default" and I didn't get
enough time to explore it fully before implementing anything. As it is
99% possible that we release further versions of DNAlive, I'll include
your suggestions and upgrade to the latest version of Jmol.
Regarding the use of the web, you can just scroll down to the
"coordinates input" and paste the sample coordinates: "chr19: .....",
then click "next step" and choose either the 3d or 4d plot. In the 3D
plot, any option is OK.
Regards,
Carles
Bob Hanson escribió:
Carles, one other comment -- For those animations I think you should
explore
load TRAJECTORY
Your animations -- basically the old simple chime-style animations -- is
precisely what TRAJECTORY is for -- the idea that all the atoms are the
same, but the coordinates change. It is immensely more efficient in
terms of memory (there is only one "model," and only the atom
coordinates change during animation). This means, for example, that you
can use cartoons (if you switched to PDB fomat), and they will properly
adjust to the changing coordinates as the animation runs -- and there is
only one set of cartoon "objects" for the entire set of atoms.
Also, right now you are using ball/stick mode for very distant views.
That decreases your rendering time. I would suggest just using sticks,
which involve less processing.
I believe you could increase the rending time substantially for these
animations.
You can try this from the console on that applet, just to compare:
load trajectory ""
Oh -- I realize you can't do that with 11.2. How about upgrading to
11.4? It has some important memory fixes, if nothing else.
Bob
Carles Fenollosa wrote:
I'm floating this old thread because I promised that I'd notify the list
when our work is published.
We've used Jmol to display DNA 3D and 4D (animated 3D) structures in our
DNA physical properties browser. It is accessible at
http://mmb.pcb.ub.es/DNAlive and will be published soon in Bioinformatics:
DNAlive: A tool for the physical analysis of DNA at the genomic scale
J.Ramon Goni; Carlos Fenollosa; Alberto Perez; David Torrents; Modesto Orozco
Bioinformatics 2008; doi: 10.1093/bioinformatics/btn259
For any of the gurus out there, any feedback on the use of Jmol will be
greatly appreciated. And thanks to the list for your help :)
Regards,
Carles
Carles Fenollosa escribió:
I've tried your method and it works great. Thanks!
El 17/02/2008, a las 21:17, Angel Herráez escribió:
Dear Jmolers,
It's been tough, but after many hours, lots of trial and error, and
error, and error, several
times despair and then a new spark, and much head scratching, I
think that I've found a
cross-browser method for exporting a snapshot of the applet into a
page (pop-up or
otherwise) from which it can be easily copied, direct from the
browser's pop-up context
menu, and sometimes even saved.
The previous one posted here by Rolf Huehne and Mauricio Carrillo is
great, but needs a
Perl script installed in the server (something no every author can
do him/herself, as I
understand the script must go to a restricted directory in the
server).
The former one, which Bob uses in his site ("show image" link under
the applet in the
demo/test pages) does not work in Internet Explorer.
This new one requires a php-enabled server only for IE, but no other
server configuration,
so you can do it all even if you are not the webmaster. Firefox and
Opera use it without php,
both online and offline. For other browsers, the two possible
methods are oferred (direct
offline, or php-online).
For now, it is at
http://angel2008.awardspace.com/JmolImageExport/
Along the next days I will add it to my site, http://biomodel.uah.es/Jmol/
, and to the Wiki,
and make it downloadable.
I will appreciate any comments and, particularly, your testing it
under non-Windows or less-
frequent browsers, so that the code can be made bulletproof.
Hope you enjoy it
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Carles Fenollosa, computer engineer
MMB Group @ INB/IRB/BSC - http://mmb.pcb.ub.es
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