Load personal PDB files

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cyberfunk
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I'm very interested in having the ability to load my own PDB files.. this would make molecules far more worthwhile for me, as an organic chemist.... as it is.. there's only so much that i'm interested in on the PDB site, but if I could load and show my own structures to others, this would be a great tool !

Brad Larson
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This is a popular request. At first, I didn't really know how to do this, because Apple has not provided us with a means of syncing data via the USB connection to iTunes and I didn't want to run a hosting service for everyone's molecules on my website. However, after seeing a few applications use Bonjour to connect to a client program via a local network, I think I'll give that a try.

I had planned to port this to the Mac desktop anyways, so what I'll do is add a means of using this desktop version of Molecules to load any file you have locally, render it on the desktop, and be able to send that molecule to the iPhone or iPod Touch over WiFi. This should get the job done, but it has some downsides. First, the desktop client will be Mac only. I don't do any Windows or Linux development any more. Second, you'll need to have both your desktop and your iPhone / iPod connected to the same local network, and be able to connect the iPhone / iPod to that network via WiFi.

I'm finishing up the integrated PDB keyword searching functionality, which I'll submit as an update along with the two new visualization styles that I've added: cylinder and spacefilling. Once that's in, I'll do some performance improvements. After all that's taken care of, I'll get on this. The tricky part will be adding support for all the different molecular file formats there are out there.

cyberfunk
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Support for many file formats can be added by using OpenBabel... also, you might include an option to type in the URL for a PDB file in case people want to access ones available via HTTP (say they make their own available to themselves via their webspace)

cyberfunk
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Brad Larson
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I've been looking at OpenBabel as an example for how to handle multiple file formats, but I don't think I'll end up using it. First, it is pretty hefty and I think some of the ways it handles files can be shortened up significantly by using Cocoa classes like NSDictionary and the XML parsing ones. Second, it is GPL, not even LPGL, so it would be incompatible with the BSD license I am putting this program out under. I want to give people the freedom to use my code wherever, and the GPL will restrict that. Also, there is some question as to whether the GPL license is even compatible with the App Store method of distribution.

I certainly don't want to reinvent the wheel on this, but just pulling in the library might not be the best way to go.

EagerEyes
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The only way to sync content from your computer directly at the moment is over a local network. Apple makes this very convenient through Bonjour, so a program on the iPhone can easily discover a computer that it can talk to (1Password does that really well, for example). So you'd need a client on the Mac side anyway, and that could do the heavy lifting in terms of data conversion (perhaps by calling something like openbabel as an external program). Don't know how this would work on a PC, but the technology underlying Bonjour is not Apple-specific or proprietary, so there probably are ways to do this (there are apparently Java libraries for that, but I don't know yet if they require special Apple bindings).

PMA
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Excellent app and the new visualization styles in 1.1 are great. I support your plan for being able to upload personal pdb files. With large proteins, it allow one to edit a pdb file (i.e. remove the side chains) to reduce the number of atoms that need to be displayed. Is there anyway you could just have a Calpha backbone trace from a pdb file as a display option?

Brad Larson
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PMA wrote:
Excellent app and the new visualization styles in 1.1 are great. I support your plan for being able to upload personal pdb files. With large proteins, it allow one to edit a pdb file (i.e. remove the side chains) to reduce the number of atoms that need to be displayed. Is there anyway you could just have a Calpha backbone trace from a pdb file as a display option?

Glad to hear that you like them. The spacefilling mode will be cleaned up significantly in the near future.

A Calpha trace would be pretty easy to do. I've added it to the list. It won't be in the next release, but I think I can get it in the one after that.

Anonymous

I m really excited to load my PDB files. Thanks for this facality.

iclb0028
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Hi I found that a very simple and fast way of uploading *pdb files to molecules is just to e-mail them to yourself and then click on the attachment and then when it says "Open in", just click on "molecules". Simples !!!

Jeremy

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