Molecule database

9 replies [Last post]
Sailor
User offline. Last seen 7 years 37 weeks ago. Offline
Joined: 03/26/2010
Posts:

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

Sailor
User offline. Last seen 7 years 37 weeks ago. Offline
Joined: 03/26/2010
Posts:

I hpe someone can help since I would like to use this database at www.uwsp.edu/chemistry/pdbs.

Brad Larson
Brad Larson's picture
User offline. Last seen 51 weeks 4 days ago. Offline
Joined: 05/14/2008
Posts:

It looks like there is something going wrong with the way that files are being downloaded from that server. There might be something different in the way that these particular documents are being served up. I'll see if I can fix it.

Right now there is no way to directly send files to the iPhone or iPad versions of Molecules, but I'm working on a solution for that.

Philippe
User offline. Last seen 6 years 31 weeks ago. Offline
Joined: 07/27/2010
Posts:

(first off I would just like to say that your app is fantastic, thanks a lot for creating it)

I too would really like some smaller molecules.

No offense meant to the large ones, they're great and all but... it would be nice to have some that are a bit more lamen, like plastics, hydrocarbons, or even just water. Not only could I show it to more people without fear that they wouldn't understand the molecules, but I suspect smaller would mean less lag as well.

Vitamines too, vitamines aren't that big, yet they would be fun to have.

hernan
User offline. Last seen 7 years 19 weeks ago. Offline
Joined: 08/03/2010
Posts:

It is not clear how to download custom molecules

For example, I would like to download antifungals from this website

http://129.128.185.122/drugbank2/drugs/DB01263/pdb/download

Please advice

Hernan

hernan
User offline. Last seen 7 years 19 weeks ago. Offline
Joined: 08/03/2010
Posts:

I figured that out. It the website does not link directly the file with extension .pdb you can download your files to your desktop computer. then run a web server in your computer (IIS, Apache) and download the files from there.

For example, I downloaded several molecules to my windows computer (c:\inetpub\wwwroot) then using my iphone WIFI conection I downloaded the files pointed to my computer with the internet server. (eg 192.168.1.10/mymolecule.pdb)

Philippe
User offline. Last seen 6 years 31 weeks ago. Offline
Joined: 07/27/2010
Posts:

What are pbd files?

bbaker
User offline. Last seen 6 years 50 weeks ago. Offline
Joined: 12/23/2010
Posts:

I teach high school science at a school where all students have i-pads. I have had some success with downloading pdb files onto Molecules by putting them on my wiki site (will supply the address to you Brad if you can help) and when I download them it asks if I want to open the file in Molecules. Some molecules it opens with ball and stick intact. Some it opens with the of balls of correct color but no sticks. Some it opens with the balls all green with no sticks. Some it tries to open but ends up going back to the original DNA molecule in the display and lists it on the list with no atoms and it not bold. Some files even make Molecules shut down. Are these bugs you are working on? Any idea how I can tell which will work well?

Brad Larson
Brad Larson's picture
User offline. Last seen 51 weeks 4 days ago. Offline
Joined: 05/14/2008
Posts:

bbaker wrote:
I teach high school science at a school where all students have i-pads. I have had some success with downloading pdb files onto Molecules by putting them on my wiki site (will supply the address to you Brad if you can help) and when I download them it asks if I want to open the file in Molecules. Some molecules it opens with ball and stick intact. Some it opens with the of balls of correct color but no sticks. Some it opens with the balls all green with no sticks. Some it tries to open but ends up going back to the original DNA molecule in the display and lists it on the list with no atoms and it not bold. Some files even make Molecules shut down. Are these bugs you are working on? Any idea how I can tell which will work well?

I am fixing a few known rendering bugs, but if you have specific files that are causing you problems, please post links to them here or email me files at contact@sunsetlakesoftware.com and I'll see if I can determine the root cause.

However, I have noticed that sometimes people find PDB files online that have missing bonds or other elements in the files themselves, which I can't do anything about when it comes to rendering them.

Philippe
User offline. Last seen 6 years 31 weeks ago. Offline
Joined: 07/27/2010
Posts:

Thank you so much for the latest update! It's fantastic, I can actually show off a model of caffeine to people! lol

I was so grateful I gave you a 5 star review in the app store. Like I said, I don't have a problem with the giant molecules but I just find these way more usable. Thanks again!

Syndicate content