Cartoon visualization and Chainbows
Thu, 07/16/2009 - 05:56
Excellent app but a bit limited for complex molecules (e.g. my favourite, 1PZN). I normally use MacPyMol and prefer the cartoon mode for visualization, any chance you could implement this? Also, the ability to change the colouring would be really appreciated, especially Chainbows (again, for large complex molecules).
Thanks
Thorsten
Wed, 10/13/2010 - 08:54
#2
This is a great program, but as a working crystallographer, it's currently too limited to be much use. I would really like to get access to the residue numbers so that one could zoom in on a particular part of the structure.
I would pay for a decent mol graphics package that runs on the iPhone or iPad!
Mon, 06/20/2011 - 12:50
#3
I'd like to request cartoon or main chain(ribbon) visualizations for pdb files. I think they would be really helpful for people trying to look at structures. I'm not sure how difficult they would be to implement but pymol can do this so it must not be too difficult.
Thanks for making molecules :)
Mon, 06/20/2011 - 13:14
#4
I'm not sure how difficult they would be to implement but pymol can do this so it must not be too difficult.
You do realize that PyMol has been under development for over 11 years? The late Dr. Warren DeLano poured himself into the project, and he was a much greater molecular modeling programmer than I am. His recent passing was a huge loss for the field, but he left behind a significant legacy in the source code for the PyMol project. I've studied some of that code to see how he did what he did, as have others, but it's far more complex than my simple Molecules application.
This is a hobby project for me that I don't get paid for. It will take a significant amount of time to implement something like this, and I don't know where I'll find that time. The new rendering engine I implemented in 2.0 took months to assemble and I can't afford to devote that much time to a single feature again in the near term.
As you can see in the comments here in the forums, others have offered to help in implementing this, but no one actually has.
Sat, 10/01/2011 - 09:33
#5
as a former molecular modeller I would like to see cartoon display, coloring by properties(polarity, lipophilicity, etc.) and the ability to focus on regions, I.e. Channels or active sites, etc. I would gladly pay for a good app that runs on the iPad since I use tools like this to show non-chemists what I am talking about...a good app is worth a thousand words...and some money :-)
otherwise it is a good app that is competing with other apps out there like imolview, etc.
Sat, 03/10/2012 - 19:26
#6
Hi there,
Although I fully appreciate the part time nature for the coding of this app, I was just wondering if you are still planning to implement the cartoon visualisation or whether it proved too much trouble to integrate?
Cheers,
James
This is a popular request (as shown here and here), but it's a little more complex to code up than the ball-and-stick model form.
I've been a little distracted by other things for the last few months, but I'm just now getting back into working on this project. I will first try to improve the rendering speed of the current visualization modes, then attempt to tackle this, but it could be a little while before I have this kind of visualization ready to go.