Control visibility of different files on applet load

Hi,





I'm trying to create a web-page to display a series of ligands docked to a receptor. I have it working now following the template of


example-mspace7, but I would like the initial view on page loading to be clearer. Ideally, I would like it to have only one ligand visible and already zoomed to the pocket. Is this possible? I have read the 'MarvinSpace Parameters and Events' docs, but it's not obvious to me from this.





Thanks





Dave

Hi Dave,





do you mean someting like in the Java Web Start examples?


http://www.chemaxon.com/marvinspace/html/webstart.html





There is a log creating process available in mspace that helps to achieve this easily. You have to create a log file that contains the required view, and add this log file as a parameter.


Unfortunately there is a refreshing problem we have to fix, so currently it's not working with applets. If you can use JWS, then it's no problem.





Creating log file:


1. import the input file


2. choose File->Create Log File, and save the file for example as log.txt. Choose 'No' for logging mouse events.


3. zoom to the pocket


4. make every display setting, like draw types, background color, etc


5. align the view


6. choose File->Log Current View


7. choose File->Close Log File





To test it restart mspace, import the input file, choose File->Process Existing Log File, and check whether all settings are ok.





Example how log parameter is used in mspace1aid2.jnlp (first image in the second row of the gallery):

Code:

<application-desc main-class="chemaxon.marvin.space.gui.MSpaceJWS">     <argument>-l</argument>     <argument>http://www.chemaxon.com/marvinspace/jnlp/1_3/mspacelog1AID2.txt</argument>    <argument>http://chemaxon.com/marvinspace/data/1AID.pdb</argument>    </application-desc>

Kind regards,


Judit

Thanks for the reply.


I haven't used Java Web Start before and am struggling to configure the server. Do you have any quick tips?





I think I need to add a jnlp mime type definition, but adding the line AddType application/x-java-jnlp-file jnlp


to my httpd.conf file doesn't help.

Are you sure that the problem is the server side? Are you sure that your browser accepts jnlps?


Have you tried our online JNLP examples? If they do not work in your browser, it means that the jnlp mime type is not set in your browser.


See our jnlp examples and installation instructions below: Marvin Applications via Internet

If the problem is really on the server side, you have to configure your web server to support application/x-java-jnlp-file for jnlp.


Please consult with the documentation of your web server how to do it.


I don't know which type of web server you have but in Google, I found a link how to do it in Apache:


http://www.mobilefish.com/developer/javawebstart/javawebstart.html

Thanks for the suggestions. I did also need to reconfigure apache, and clear my browser cache.





The file visibility selection works in the web start MarvinSpace, which is great.





I also wanted to control the atom visibility. In the MarvinSpace session I used to create the log file, I also hid all atoms further than a certain distance from the ligands. But this information doesn't seem to have been logged. Is this not scriptable?





Thanks





Dave

Hi Dave,





apologies for not replying earlier.


You're right, atom visiblility is not correctly recorded, we'll fix this.





The visibility of whole structures, and the "Zoom to pocket" function works now.


So they say, the zoom to pocket function is not comfortable enough to use, because the range cannot be controlled. What do you think about it?





(Btw. the default distance is 4 Angstroms from the bounding box of the ligand on which it is used. Residues will not be partially hidden, so all residues stay visible that have at least 1 atom in the pocket range.)





Regards,


Judit

Hi Judit,





Thanks for the message. I think it will best if


all settings in the viewer are logged in the script,


so that a view can be recreated.


Can these scripts also be loaded into MarvinSpace applets?


It would be nice to be able to switch between different views


using html elements + javascript calls.


(Sorry if some of these features exist, I am not an expert.)





Also, I'd support the suggestion of making the pocket radius


adjustable. Sometimes you have a small ligand in a large pocket,


or you just want to see more of the neighbouring residues. I typically


use 6A, for example,as well as then expanding selction to all atoms in selected residues, as you say.





Thanks again,





Dave

Hi Dave,





thank you for your answer.


The scripts can be loaded to applets, but the view settings are incorrect for some reason. I guess the applet resets the view after reading and processing the view settings from the log file. It has to be corrected.





Setting the pocket radius adjustable is an easy improvement that can be implemented fast, we'll definitely do this.





We have to discuss internally when can we implement the missing functions, i.e. adding atom visibility to logs and correcting view settings in case of applets.





Kind regards,


Judit