News for Jmol for Folding At Home

[NicoV]

Hi everyone,

A few news about Jmol and also its use for Folding At Home - http://www.jmol.org/fah/

First, the new stable version 11.6 has just been released today
The announcement: https://sourceforge.net/forum/forum.php?forum_id=872607

Second, sourceforge has changed how updating of the website is done.
I didn't have the time to change my scripts, so I haven't been able to update it in the last weeks.
Need to find time.

Third, Bob Hanson, the main Jmol developper, has added a reader for Amber molecular dynamics and it works with files produced by the Amber core
This feature is available in the new development releases (11.7) only and not in the stable branch (11.6). Jmol 11.7.1 is already available.
An example of a command to load an Amber WU in Jmol :
load FILES "D:/Fah/p4606_98/wudata_08.top" COORD {0 -1 1} "mdcrd::D:/Fah/p4606_98/wudata_08.trj"
and you can then animate it with:
anim on

I have to modify the website to take advantage of this new feature, once I find the time.
But we can still start to gather Amber files, and there you can help me

Each Amber wu produces 2 interesting files, a topology file (.top) and a coordinates file (.trj).
Apparently, each 2% a new set of coordinates is added but unfortunately the files are deleted when 100% is reached.
So, I need the .top and .trj files with a maximum of % done (for maximum number of frames, 98% or 99%, which gives 49 frames)

Currently, I already have :
p4597: 98% (done)
p4599: 98% (done)
p4603: 98% (done)
p4606: 98% (done)
p4608: 70%
p4617: 90%
p4618: 56%
p4624: 57%

Nico

[NicoV]

Second, sourceforge has changed how updating of the website is done.
I didn't have the time to change my scripts, so I haven't been able to update it in the last weeks.
Need to find time.

Done

[NicoV]

Currently, I already have : ...

The list of Amber projects I already have is kept updated at http://www.jmol.org/fah/availableAmber.txt
The list of Amber projects I am looking for is kept updated at http://www.jmol.org/fah/missingAmber.txt

[NicoV]

I have just upgraded the tool that checks in folders to find missing files : it can now send topology and trajectory files produced by the Amber core.
https://sourceforge.net/project/showfil ... _id=223033

It's a Java program, so you need Java on your computer.
To use it, unzip the files, double-click on JmolFah.jar (or execute java -jar JmolFah.jar), configure the tool (mail, username, ..., directories) and let it check for interesting files.
If you want, you can create a scheduled task (or equivalent, depending on your OS) to run it on a regular basis (every hour, every day, ... up to you)

[NicoV]

I have released a new version of the tool for checking missing files (v0.8) : the tool can now keep working in the background, waking up at regular intervals to check for missing files. Two intervals can be programmed : one by default, and one that is used when a missing amber project is nearing the 98-100% completion.
https://sourceforge.net/project/showfil ... _id=223033

No more need for scheduled task

[anandhanju]

Is there is a minimum version of Java needed for this? I see this exception:

Code: Select all

C:\Documents and Settings\abhat\My Documents\FAH\Util\JmolFah-0.8>java -jar JmolFah.jar
Exception in thread "main" java.lang.NoSuchMethodError: java.lang.Integer.valueOf(I)Ljava/lang/Integer;
        at org.jmol.fah.checkxyz.ConfigurationWindow.createFieldsComponent(Unknown Source)
        at org.jmol.fah.checkxyz.ConfigurationWindow.createPreferencesComponent(Unknown Source)
        at org.jmol.fah.checkxyz.ConfigurationWindow.createWindowContent(Unknown Source)
        at org.jmol.fah.checkxyz.ConfigurationWindow.<init>(Unknown Source)
        at org.jmol.fah.checkxyz.Check.configure(Unknown Source)
        at org.jmol.fah.checkxyz.Check.process(Unknown Source)
        at org.jmol.fah.checkxyz.Check.process(Unknown Source)
        at org.jmol.fah.checkxyz.Check.main(Unknown Source)

C:\Documents and Settings\abhat\My Documents\FAH\Util\JmolFah-0.8>

The Java version I have is:

Code: Select all

C:\Documents and Settings\abhat\My Documents\FAH\Util\JmolFah-0.8>java -version
java version "1.4.2_11"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.2_11-b06)
Java HotSpot(TM) Client VM (build 1.4.2_11-b06, mixed mode)

[NicoV]

Yes, I have developed it with 1.5 and I am using several 1.5 features (generics, ...)

[NicoV]

I have released a new version of the tool for checking missing files (v0.9) : the tool can now also save interseting files in a local directory, enabling it to do its work even when not connected to the net.
https://sourceforge.net/project/showfil ... _id=223033

(0.9 is broken, use 1.0)