MarvinSpace 4.1.6 (Test Version)

Hi, it's been a while. Hope you can feel the spring is coming.





I've downloaded the test version that you've uploaded last time. Thanks, it improved greatly, except a couple of concerns (sorry, again).





I've tested MarvinSpace with protein/membrane complex of PDB entry 1uyn and DMPC lipids.





1. bond between distant atoms (see attachment, picture 1.png and step5_assembly_ms.pdb)


Two line between distant headgroups of two lipid molecules in each of the membrane leaflets.





2. pdb with many water molecule


We used to reduce the number of water molecule to 1/2 or 1/4, and it works fine with those pdb with reduced number of water. But we failed to open a pdb if we don't reduce the number of water molecules (both of the applet and marvinspace app). Here I attach the pdb file (step4_lipid.pdb).





3. secondary structure chain color


When can we have a secondary structure with chain color enabled?





4. can marvinspace call a javascript function?


This is a question. I want to know whether can marvinspace call a javascript function, with residue id as an argument, when a user click an atom.





p.s.


I saw that you go for the ACS National meeting this month. We also go to the meeting and will have a poster session. Hope to see you guys at there. :)

Hi Sunhwan, good to hear from you:)


We're glad for all the feedback!





1. We try to fix this soon.





2. It's the memory consumption. We'll increase water storage efficiency, until that increasing jvm heapsize can solve this.





3. Sorry, could you explain this in more detail? I'm not sure what you mean, for example to define different chain colors programatically?





4. Sounds interesting, let's discuss this. We haven't done it yet, though it would be possible. Can we ask about the goal?





5. I forgot to tell that the 4.1.6 version uses a new Jogl. This means mspace requires a new jar file, gluegen-rt.jar. Hope this is not causing any problems.





6. The ACS National meeting: Miklos and myself won't be there personally, but chemaxon will have a booth and our collagues will welcome you!





Judit

Quote:

3. Sorry, could you explain this in more detail? I'm not sure what you mean, for example to define different chain colors programatically?

If you look at the attachment "Picture 1.png" that I posted yesterday, the secondary structure has only one color. But it suppose to have two color (helix in center and outer helix) based on MarvinSpace app (not in applet). We turned on secondary structure coloring by chain.





document.MSpaceApplet.setProperty("SecondaryStructure.ColorType", "Chain");"





Am I doing something wrong?

Quote:

4. Sounds interesting, let's discuss this. We haven't done it yet, though it would be possible. Can we ask about the goal?

We want to remove some of the residue in pdb (explicitly, water molecule). So what I've thought is, if marvinspace applet invokes a javascript event, which can pass the residue number to the HTML form.





So, to be in general, I think it would be great if marvin space applet supports javascript event handler, so that match javascript functions with marvin space event, such as when a residue selected by user.

Quote:

5. I forgot to tell that the 4.1.6 version uses a new Jogl. This means mspace requires a new jar file, gluegen-rt.jar. Hope this is not causing any problems.

So far, I don't see any further problem. Thanks





Sunhwan

Nothing seems wrong. Chain coloring (as well as identification) uses chain information (chain id) from the pdb file.


That structure is colored by one color because it has only one chain according to its pdb file.





We'll get back with the javascript issue soon.

Judit wrote:

Nothing seems wrong. Chain coloring (as well as identification) uses chain information (chain id) from the pdb file. That structure is colored by one color because it has only one chain according to its pdb file. We'll get back with the javascript issue soon.

I was curious because the applet doesn't color helixes, but the marvinspace app (mac) colors helixes with different color. Check the attached image.

Ah, I see! Something is wrong with chain coloring on mac then:)


It is the default secondary structure coloring there.


The inner helix is colored red, as helices, but the outer 'helix' is green because it is composed of beta-sheets.


This secondary structure should be white with chain coloring like on the previous picture you attached.