Re: [Jmol-users] residue highlighting

Helix Photon Sat, 22 Sep 2007 19:11:52 -0700

Thanks Hatuey for the help,
 I have one query, i am developing a webpage and using Jmol, I want to display 
a protein structure.
 the important thing is when the applet will load the protein it should 
highlight one of the residue in spheres with different color from the protein.
 I was wondering if this could be possible in jmol and if possible, then how do 
i script for that, means which functions to use.

thanks
helix

Hatuey <[EMAIL PROTECTED]> wrote: If your system has more than 4Gb of RAM
memory, you should continue with your 64bit Linux, as 32bits operative system
can handle only up to 4Gb.

I have a two AMD Opteron 64bit dual core processors running Fedora 32bits (with
2Gb RAM). I am running chemistry quantum computing soft like NWChem, Gamess-US,
and of course, Jmol without a problem.

The only thing BAD is that as I have the source of NWChem and Gamess-US, I can
compile them to run in 64bits and get the full advantages of 64bit computing,
so the calculations can run at almost twice the speed for 32bits.

Regards,

Hatuey

On 9/21/07, Helix Photon <[EMAIL PROTECTED]> wrote: Hi Hatuey and Raphael A.
Bauer

Thank you for your valuable suggestion and I also think that I must format the
hard disk and install the 32 bit version of Linux(may be Ubuntu or fedora or
suse).
>From morning, I tried all the possible permutations and combinations
>(tutorials and forums) to load the applet but all failed.

Just one last suggestions,
This is my machine configuration:
Dell Precision 390n mini tower PC Processor E6300, 1.8 GHz, 10662MB L2, DC/VT,
3GFC2C1.
2GB, 533 MHz, DDR2 ECC SDRAM
128MB PCle x 16nVidia Quadro NVS 285 dual VGA graphics.
Linux v4Intel EM64T 64 bit

and I don't run very high memory > 4gb applications, so I was just wondering if
the installation of 32 bit won't cause any problem in the machine.

thanks
helix
PS: I have MySQL database and related PHP as the major application running.

Hatuey < [EMAIL PROTECTED]> wrote: Hi all,

The problem with Jmol in 64 bits is not a problem of Jmol. It is a problem of
Java+Linux+64bits combination.

I tried all the tutorials, tips, etc. found googling about setting up Java in
Linux (I am using Fedora 7) without success. My solution? Install a 32bits
Linux version in my 64bits box :( everthing work fine!

Regards,

Hatuey

On 9/21/07, Helix Photon < [EMAIL PROTECTED]> wrote: Hi Egon,
I am using Ubuntu 7.04 for 64 bit machines and I am using Firefox version
2.0.0.6 as the web browser.
regarding the plugin, when I tried to install it showed me this:

sudo apt-get install sun-java6-jre sun-java6-plugin

Reading package lists... Done
Building dependency tree
Reading state information... Done
sun-java6-jre is already the newest version.
sun-java6-jre set to manual installed.
Package sun-java6-plugin is not available, but is referred to by another
package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
E: Package sun-java6-plugin has no installation candidate

So, how do in install these.
thanks
helix
Egon Willighagen < [EMAIL PROTECTED] > wrote: Hi Helix,

On 9/21/07, Helix Photon wrote:
> I was wondering if Jmol could be loaded on 64 bit, Ubuntu linux machine.
> When I tried to open the demostration page, it showed me Applet loading and
> then for 1000's of seconds elapsed and it didn't load the applet.

Should be no problem. Which Ubuntu version are you using? Did you
install the Sun JVM (apt-get install sun-java6-jre sun-java6-plugin)?
Which browser are you using?

Egon

--
----
http://chem-bla-ics.blogspot.com/

-------------------------------------------------------------------------
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2005.
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users

---------------------------------
Don't let your dream ride pass you by. Make it a reality with Yahoo!
Autos.

-------------------------------------------------------------------------
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2005.

http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users

---------------------------------
Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel
and lay it on us.

---------------------------------
Be a better Globetrotter. Get better travel answers from someone who knows.
Yahoo! Answers - Check it out.

-------------------------------------------------------------------------
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2005.
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users

---------------------------------
Check out the hottest 2008 models today at Yahoo! Autos.

---------------------------------
Got a little couch potato?
Check out fun summer activities for kids.

-------------------------------------------------------------------------
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2005.
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/

_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] residue highlighting

Reply via email to