[Jmol-users] Experience of finding Visualisation tool to replace Chime/rasmol

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Hi Everyone,

Thought you might be interested in some feedback I was giving the Jmol 
Developers in regards to my efforts to find OR develop a replacement for 
Rasmol/chime to be used to teach protein structure and functional chemistry in 
our medical science / biotechnology degrees at our university. 


Hi guys,

I built a vis tool using java 3D extension but the performance (frame rate) 
above 4000 coordinates was very poor... even after removing antialiasing and 
other taxing processes.  We also looked at pymol, molView, FPV, cn3d (C++), 
mage/kinemage (Java - from Richardson lab at Duke Uni.) and of course rasmol 
and chime.

The major deficiencies of all of these included: 

1) excellent quality images in 3D space with really nice rendering, but when it 
came to interacting with the molecule, performance (frame rate) was very poor 
for large molecules (such as over 50,000 coordinates, I tested with a 59,000 
coordinate structure file using spacefill/vdw representation, apparently there 
are some files already that have greater than 99,999 coordinates, so the need 
to handle large files was important) OR when you were at maximum zoom and 
rotating the molecule with a mouse.  So rotation/translation was very clunky on 
those apps with nice graphics.

2) Those programs that could handle smooth rotation/translation of the very 
large structures had very, very poor quality graphics.  So if you used one to 
visualize an interaction/characteristic of a molecule and wanted to use it in a 
presentation - it would look very second rate... and the aim of the software is 
visualization... so poor quality rendering/buffering of the image was also a 
key requirement !

3) Functionality and the ability to take command line inputs was essential - 
especially for teaching.  It just provides versatility in working with 
molecules and allows the running of scripts.

4) portability because we have people with Mac's and PC's and Linux machines !


SwissView is also a program we use and considered, but it requires a lot more 
time to teach with because of the large and advanced function range it 
possesses, so is more suitable for teaching people already skilled with 
rasmol/chime/jmol. And it’s a predominantly point – click format also.  

I actually tested the old V8 of Jmol and was a bit disappointed by it's 
performance in No. 1 above, But when i checked out the V10 beta code and 
compiled it, blitzed No. 1 requirement above !!! Jmol is a long way ahead of 
any other open-source vis application I found, in all 4 area's above !  The new 
graphics engine is excellent.  And the specular and perspective used for 
visualizing the structures contributes alot to the realism of the images.  
There are other features that would be nice, but I’m sure their on there way 
(solid ribbons, solid ribbon cartoons, iso-surfaces etc).

So I was really excited by V10 Jmol !.. We also have SGI machines in the school 
we use for rational drug design but these aren't any good for teaching 
biochemistry secondary/tertiary structural protein chemistry as Rasmol/chime 
were.

I’ve modified Jmol application V10 code to include a summary of the PDB file, 
which collates all the information for each molecule represented (expression 
system, chain identifiers etc) which can be saved as an .rtf; a window for 
viewing the entire raw PDB file (without having to open it in third party app), 
and a window for reading collated PDB file remarks. 

I docked the script window with the graphics panel and put the measurements 
panel behind it on a tabbed panel.  I also added a browser pane to it where we 
will have tutorials. I'm just updating the browser window so it's http 1.1 and 
javascript compatible and can authenticate, and we’re still to write the actual 
tutorials for the browser window.  So it’s heavily geared for educational 
purposes and providing as much information to the user about the structure as 
possible, as well as easy access to essential functions – measurements and 
command line.

There are some screen shots of what we’ve come up with so far located here

http://jmol.sourceforge.net/dchandler/screen_1.jpg
http://jmol.sourceforge.net/dchandler/screen_2.jpg

... still 2-3 months away from finishing it up (as I’m doing a PhD in Molecular 
Biology – crystallography studies of a protein, and doing the programming just 
on the side in my spare time... PhD + sparetime = not enough hours in the 
day !).  

Hope this gives you some ideas and info on where we think Jmol stands as a tool 
for protein / molecular visualization, and it’s excellent applications as a 
tool to replace rasmol/chime !

best regards

Dave Chandler
 
PhD Student
Australia