[ Jalview 2.6 built 26 Sep. 2010 ]
i have a .seq i'd like to align with an extant stamp structural alignment.
before i re-do this in Jalview, it'd be nice to know if Jalview will
take any of the stamp output.
-bryan
Hi Bryan, sorry for the delay in responding. I've been in meetings over the last few days.
i have a .seq i'd like to align with an extant stamp structural alignment.
before i re-do this in Jalview, it'd be nice to know if Jalview will
take any of the stamp output.
If I remember correctly, Stamp is capable of generating a multiple sequence alignment based on the structure alignment that it calculates. However, I'm not at all familiar with Stamp's command line arguments, so I couldn't tell you how to do this.
At the moment, this would be the only way to get stamp output into Jalview. After that, you just need to add your sequence to the alignment window, and use the 'Clustal Realign' web service to align the sequence to the existing set.
Also, once you have the alignment in Jalview, you can load the pdb files you are interested in on to their sequences in the alignment, and then use the built in Jmol to view the superposition. The poses will not be as accurate as as stamp's superpositions, since Jalview only superposes the alpha carbon atoms of aligned residues, but they will certainly be enough to get a feel for the conservation patterns w.r.t. your new sequence.
Jim.
···
On 15/11/2010 21:26, Bryan Lepore wrote:
--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.
Hi,
I wanted to know if there is a possibility to add a parameter file to the jalview applet ?
I know for the features and annotation files, but I'd like to start the applet online with some parameters for the view (hide conservation annotation line, stuff like that) and I would like to put this parameters in a file, so when someone downloads the applet to run it locally (with annotation file, features file and possibly parameter file), the same view is presented for him, with my viewing options.
How can this be done ?
Thank in advance,
Balazs Laurenczy
Hi Jim
thanks for your comments - Geoff suggested i try the .blc without the
"#" and that didn't work, however a .msf laying around did - not sure
if thats from stamp, but anyways, looks like i'm back on track.
-Bryan
die hard STAMP fan
wait - i found another .blc file i think, seems to work.
i think my stamp script needs some editing.
-Bryan
Hello Balazs,
I wanted to know if there is a possibility to add a parameter file to the jalview applet ?
Not as such - the only flavour of Jalview that supports a properties file is the Jalview Desktop.
I know for the features and annotation files, but I'd like to start the applet online with some parameters for the view (hide conservation annotation line, stuff like that) and I would like to put this parameters in a file, so when someone downloads the applet to run it locally (with annotation file, features file and possibly parameter file), the same view is presented for him, with my viewing options.
If you only want your users to be able to view your data in the applet, then the properties controlling the display and automatic annotation can all be set from the parameters passed to the applet when it is launched - so, the initial html page becomes your properties file. The parameters are all documented on the applet parameters page:
http://www.jalview.org/examples/appletParameters.html
If you want to launch the application with a specific set of default display settings then things are a little different. You can supply a properties file on the command line, and these will be used instead of the user's default ~/.jalview_properties file. Then, all you need to do is prepare your view defaults using the preferences dialog box, then make a copy of your preferences and edit it to remove any personal information (file name history, etc) before putting it online. Take a look at the application command line arguments for more information, here http://www.jalview.org/help/html/features/clarguments.html
Is that along the lines of what you want to do ?
jim.
···
On 19/11/2010 10:26, Balazs Laurenczy wrote:
--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.
Hello Balasz.
File annotation interpretation isn't working the same between the applet and the JavaWebStart version : when interpreting my annotation file, the applet version seems to have a bug.
hm. I was about to open a bug report about this, but then when I took a closer look at your annotation file fragments I noticed that they don't actually correspond to your screen shots. Could you send me *exactly* the files you used ? Then I can see exactly what's going on. Even better, feel free to register and create a new bug report at issues.jalview.org
Another issue I am having is to associate sequences with annotation rows. It works perfectly with the webstart version : if I click on an annotation row's label, it highlights the associated sequences.
But I'm unable to do so with the applet, both mouse buttons (right and left click) on an annotation row label's opens a popup dropdown menu and doesn't highlight anything.
Is it possible to add this feature to the applet version ?
Ah - I'd forgotten about that! I've made a note about this here http://issues.jalview.org/browse/JAL-484
I'll also try and get it implemented for the next release (2.7).
And my last question would be : is there some documentation available about customizing the .jlnp file for the web start version of jalview ?
Not yet - its probably time to start some. However, most customisation is pretty straightforward. All you need to do is download the latest jalview jnlp file from www.jalview.org/webstart/jalview.jnlp , and insert the appropriate Jalview command line arguments as <argument>...</argument> within the 'application-desc' tag of the Jalview jnlp file. The command line arguments themselves are documented here: http://www.jalview.org/help/html/features/clarguments.html
Two other things to rememember:
1. where there is a parameter that takes an argument, you should specify the parameter and its argument in separate <argument> tags, e.g.:
<argument>-open</argument>
<argument>myalignment.fasta</argument>
2. The jnlp file is an XML document - that means that you may need to translate URLs and other arguments containing special characters into the documents encoding (which is usually UTF8 these days).
Jim.
···
On 03/12/2010 15:57, Balazs Laurenczy wrote:
--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.