Slab addition

>>>>Just to clarify: all chains are displayed in the current implementation, but the chain identifiers are dislayed as A, B, C etc, but you'd like to see PROA, PROB etc on the right hand side selection panel. Is that correct?


Or you mean that some chains (i.e. atoms, bonds) are completely missing from the 3d view?





Sorry about the late reply. Right now, Mspace only lists the chains from the parent protein in the PDB file(in Crystals). Charmm uses the pdb file and duplicates the protein chains in specified coordinates to produce a crystal. Now Mspace, only lists the chains from the parent protein. It does not lists the chains from the duplicate copies (C001, c002 etc..) although we can see this in the 3d view, it isnt listed in the right hand side. It would be great if mspace lists all the chains.





>>>We will check this (later). Probably knowing your browser + operating system would be useful information.


We are experiencing the problem with both Mac and Windows XP, IE,Safari and firefox.





Also, we are adding a functionality into charmm which needs one more feature in mspace. We need to add a function called slab addition. Based on 4 coordinates, mspace must draw a slab in the pdb. Am i explaining it right?





We must be able to add n number of slabs at any given coordinate.





Please let me know if this is possible, I would be happy to explain more if you have questions.





Thanks


Vidyashankara

Hi Vidyashankara,

Quote:

Charmm uses the pdb file and duplicates the protein chains in specified coordinates to produce a crystal. Now Mspace, only lists the chains from the parent protein. It does not lists the chains from the duplicate copies (C001, c002 etc..) although we can see this in the 3d view, it isnt listed in the right hand side. It would be great if mspace lists all the chains.

O.K. clear, and this has been implemented. Now all chains are recognized and the long (4 letter) names are used in the component panel.





The visualisation of the secondary structure has also been improved, the infinite lines are not drawn anymore. However, since the main chains are sometimes scattered, there are distant backbone atoms that are still connected with a long curly line, we'll fix that too.





Meanwhile, we are working on the secondary structure recognition based on the backbone atom coordinates, there is some progress with the helices.

Quote:

Also, we are adding a functionality into charmm which needs one more feature in mspace. We need to add a function called slab addition. Based on 4 coordinates, mspace must draw a slab in the pdb. Am i explaining it right?

To draw such slabs on the drawing canvas should not be a problem. How is the slab defined? In the PDB file or via API calls, via GUI/menu item?


Do you also need to export such PDB file from mspace, or display only?





Regards,


Miklos

Thanks for implementing the new chain recognition system!





The slab is defined by api. so we need a parameter like


document.MSpaceApplet.slabcoor(x1,x2,x3,x4);





where x1, x2 ,x3 and x4 are coordinates in this format (x1,y1,z1)





eg


document.MSpaceApplet.slabcoor((x1,y1,z1),(x2,y2,z2),(x3,y3,z3),(x4,y4,z4));





is that clearer? If it not, please let me know and i would happy to get indepth!





Also, the pdb file must just be displayed. users will be able to download the modified pdb from our website.

Hello,





we'd like to test the recent changes a bit before doing the new release, hope it's not a problem.





Could you explain what do you mean by a slab? Is it a clipping plane (like in Rasmol) or a slice from the electron density or can you give us a picture that shows a slab?





Judit

I think you are refering to a slab in rasmol, which cut a certain


portion of your protein.


(You can try it to see what I meant). Anyway, we can use this as an


opportunity to include such a


feature in electrostatic potential visualization. So, we are asking two


slab modes.





(1) show them a following link for visualization of electrostatic


potential with a slab mode.


http://www.dino3d.org/tutorials/?p=pot





(2) we need a tool to draw lines (as shown in the attached file) and


possibly fill the ares formed by more than three lines





Please let me know if you need more explanation!

Ok, so there are two slab modes


(1) this cuts the surface like in Dino, and leaves the others?


Can you please visit www.chemaxon.com/marvinspace/slab?


If you select a surface inside marvinspace through the popup menu in the selection panel, there will be 6 clipping planes that will cut the surface.


It can be moved around by clicking the 'move' control button on the toolbar, and dragging with the mouse.


Is that what you mean?





(2) What would you like to fill the area with, and how would you like to set it?





Thanks,


Judit

Hi Judit, Sorry about the late reply.


1. The slab must be defined by the values given by the parameter.


2. The area must be transparent.








Is that clearer?





Can you tell me about hoe long it will take to implement the slab mode( the one i showed on the sample picture)? You will need to take values from a parameter and then add lines joining those points to make a plane in the protein.

Ok, that's clear now.


We will try to implement a version this week and make it available as an applet example (as usual), so you can check easily if it needs more refinement.


Judit

Well, let's see if it is clearer:)


Can you please visit: http://www.chemaxon.com/marvinspace/slab





There is a new api function:

Code:

document.MSpaceApplet.createSlabComponent(float[], float[], float[])

This creates a Slab based on 4 points, each having 3 coordinates.


The slab is simply drawn as lines between the points.


In the example the color and the name of the slab is also set:

Code:

var sc = document.MSpaceApplet.createSlabComponent(v1, v2, v3, v4); sc.setName("Slab"); sc.setColor( new Packages.java.awt.Color(0, 1, 1) );

The Slab also appears in the Selection Panel on the right, visibility and selection works properly.





Is this what you meant? Is there any more that should be done or would be good to have?

Hi Judit,


We love the new feature. Its perfect. Is it possible to add a transparent colour to the slab? like it should be filled with a semi transperant white colour.Is that possible? and when will the new applet be available for download?





Thanks


Vidyashankara

Hi Vidyashankara,





I've updated the applet to draw a transparent slab. The transperency value can be set by

Code:

sc.setTransparency(float v)

Is it ok if the area is always white, or should it be the same as the set color?





As far as I know, Marvin is going to released today or tomorrow, it will be available then.





Best regards,


Judit

Hello Vidyashankara,


The test version can already be downloaded from http://www.chemaxon.com/test/marvin/download.html.


Judit

Hi Judit,





We have finished testing Mspace pretty intensively over the last few days. We found a few issues with the test release that we downloaded. They are :





1. Slab is not working on Mac OS.


I am using Mac OS X 10.4.8, Intel iMac, and Java 1.5.


Either Safari 2.0.4 and Firefox 2.0 don't display the slab.


(Safari died and firefox freezed when I open the page.)


- Add:


Firefox 1.5 on Windows XP is ok, but IE 6 got an error


"createSlabComponent: no such method exists"





We cant view the slab component in mac, and IE. it works only in firefox. Can we fix that?





2. More on slab functionality


We want to draw not only rectangular, but also various shapes like hexagonal


or octagonal. So, it will be wonderful if we can draw line and connect each line


as a slab component.





So, we can have a parameter like


document.MSpaceApplet.createSlabComponent(v1, v2, v3, v4, v5, v6, v7);


and mspace must connect all these points to make a plane.





3. Lipid discrimination


We are building membrane/protein complexes. So, a protein would be surrounded


by lipid molecules. To get a better image, we hope we can change the display


options (such as, ball radius, bond width, and etc) for the lipid molecules.


We thought if we changed ATOM keywords to HETATM for lipid atoms, mspace


would recognizes them as a ligand. However, it turned out it really slowed down


the mspace applet. It will be great if we have a lipid section in the


option window


and parameter so that we can change its ball radius or bond width, etc.


(here I attach a pdb containing lipid molecules, DMPC.)





If you have any questions, please dont hesitate to ask me.





Thanks


Vidyashankara

Hi Vidyashankara,





glad to hear the good news.





1. Judit will fix that soon.





2. What about methods like these:





MSpaceApplet.beginSlab();


MSpaceApplet.addSlabCorner( x, y, z ) ; // suggest better name plz


MSpaceApplet.endSlab();





This gives flexibility, it is clear and easy to use. What do you think?





3. HETATM is troublesome in marvin (I can explain why, if you are interested...)


If, however, this is the only way you think this problem can be tackled, we chage some internal representations...





Can't you use the extra chain id for that purpose? Beside PROA, PROB etc and C001 etc why don't you use LIP1, LIP2 etc? What do you think?





Best regards,


Miklos

Hello Vidyashankara,





1. sorry about it, I can reproduce it and I'll try to fix it soon.





2. I'd suggest some more possibilities, such as


document.MSpaceApplet.createSlabComponent(float[][] vertices)


or


document.MSpaceApplet.createSlabComponent(float[] vertices).


In the latter case the x y z coordinates are following each other, so the number of vertices is one third of the array length.


For the first test these are working very well.





Which one would be more convenient for you? Multiple solutions are also possible.





Judit

Can you check it again, please?


Now it works on several computers and browsers here, but I couldn't test it on Mac yet.





http://www.chemaxon.com/marvinspace/slab/





Setting >=3 vertices should also work.





Judit

Hi Judit/Miklos,


1. The applet is working on IE and Mac now. Thanks for fixing it. Could release the new version for download?





2. can we use the following param?





MSpaceApplet.beginSlab-name=slab1();


MSpaceApplet.addSlabCorner( x, y, z ) ;


MSpaceApplet.addSlabCorner( x1, y1, z1 ) ;


MSpaceApplet.addSlabCorner( x2, y2, z2 ) ;


MSpaceApplet.endSlab();





MSpaceApplet.beginSlab-name=slab2();


MSpaceApplet.addSlabCorner( x, y, z ) ;


MSpaceApplet.addSlabCorner( x1, y1, z1 ) ;


MSpaceApplet.addSlabCorner( x2, y2, z2 ) ;


MSpaceApplet.endSlab();





We just need to add a var for the slab name which will appear on the list on the right hand side.





We will try to use an extra chain id for the lipid discrimination and get back to you with that.





I hope you are having a nice time over the holidays.


Happy thanksgiving,


Vidyashankara

Hi Vidyashankara,





1. a new release is planned this week, we will try to urge it, and get back soon.





2. do you mean you'd like to give the slab name as argument, like


MSpaceApplet.beginSlab("Slab1");...?


We will do the necessary modifications for the release.





Thank you very much, the same to you!


Judit

The latest version (not released yet) on http://www.chemaxon.com/marvinspace/slab/ uses the following:





These are all available:

Code:

MSpaceApplet.createSlabComponent(); MSpaceApplet.createSlabComponent("SlabName"); //sets name of the component MSpaceApplet.createSlabComponent("SlabName", 0, 255, 255); //sets color too

Adding arbitrary number of vertices by:

Code:

slab.beginSlab(); for(i = 0; i<n; i++) {     slab.addVertex( xi, yi, zi ); } slab.endSlab();

Please note, that the full jsp+html source code is available on the test page.





We will launch it if it is ok for you.


Regards,


Judit

Looks perfect :) We love it!





When is the release coming out?





Thanks


Vidyashankara

The personnel who is responsible for releases plans the next patch release for tomorrow.


Hope, that it's ok.


Judit

Hi Judit,





I just wanted to know if the other slab mode is added. remember the one in dino? where the electrostatic mapped conolly surface is cut at a certain point. if thats added, can you give me the parameter? Thanks


Vidyashankara

Hi Vidyashankara,





Is there a connection between the 2 slab modes (cutting the surface by the current slab)? Or would you like to have another parameter to define a clipping plane?





What would it cut, everything, or just the surface?





Thanks,


Judit