General discussion

Perhaps I missed it, but I couldn'nt find any information of how to create custom molecules. I really would like to use this to teach basic molecular structure of some of the more simple molecules. Are there any tools to build molecules in the correct format? Thanks!

Good morning Brad. I would like to thank you for the Moecule software. I was pleased and surprised to find it. I have found a data base(pdb format ) for small molecules, polers, and biological molecules. However, when I query it it just returns the file title with no sign of the molecule. I thought you could help. Also, is there any way to sync a model database file fromy pc to molecules? Thanks again for the software and your help. Paul

Is there any chance of a Mac version of this software. If not, is there any similar software for mac?

Hi,

My name is James Jack, I'm a consultant working for Symyx (formerly I worked for MDL) in the UK.

I've written an iPhone application which performs name searches for structures using webservices like the DiscoveryGate webservice and ChemSpider. Currenly structures are rendered as 2D PNG images. There are a bunch of other webservices I plan to add.

Would there be any interest in extending Molecules to work with 3D molfiles? The DiscoveryGate webservice offers molfiles with 3D coordinates.

Hi Brad,

Can you set up the RSS feed for your main stories? I'd like to add it to my email client's news aggregator.

I would like to have the option to see phosphorus in green.

Okay, I know this isn't a standard way of coloring phosphorus, but the NCBI uses green and it's nice because it's easier to see the contrast between oxygens and phosphorus in DNA and RNA.

Some of the other Cn3D coloring options would be nice, too. Some examples are: rainbow (colors ROYGBIV from 5' to 3' or amino to carboxyl), charge, temperature, hydrophobicity, and sequence identity (for aligned proteins).

I'm new to OpenGL ES (and Obj-C) and am trying to figure out how to subdivide & texture an icosahedron.
I came across the Molecules source-code, and have been using your source-code as a reference.
There's one thing I can't figure out - what code would you add to subdivide your icosahedrons even more? I have read the Red Book procedure, but I cannot translate it into ES.
Seeing as I'm only interested in rendering one sphere object, cpu/gpu shouldn't be a constraint.

Just thought I'd mention that WordPress has released the source code for their iPhone application. There is also some hoopla over a course that will be taught at Stanford on iPhone programming. Especially the latter makes it appear likely that the NDA will be lifted soon.

WordPress is also a big enough target for Apple to take down if they're really serious about it. So if nothing happens for a week or two, I think we'll see a lot of opening of iPhone source code.

What other interesting molecules have folks found in the Protein Data Bank? So far I've downloaded a couple of ATP synthase models - 1qo1 (3912 atoms) and 1e79 (25224 atoms) which slow down the program a wee bit but are interesting to explore. I'd like to find a way to download smaller ligands like caffeine as well.

Thanks,

Mark