Molecules 1.3.1 submitted for review, fixes search crashes

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Now that I'm back from the holidays, all immediate issues are taken care of here at work, and iTunes Connect is back up, I've submitted version 1.3.1 of Molecules for review (and updated the source code. This is a bugfix version, addressing the recent crashes when trying to search the Protein Data Bank. The PDB servers stopped responding to one half of the search query I was sending, which was a condition I had not anticipated, and Molecules would crash as a result. Unfortunately, until they fix the server response, the search results will no longer list the titles of molecules.

I apologize for any problems this has caused. I was stupid not to anticipate this kind of response.


The new molecules reports that it cannot retrive the titles only the codes

Yes, unfortunately that part of the query is still not succeeding. However, the people at the PDB are working on a fix for that.

I'm going to switch to using a more robust search API in the next version, which will also provide a fix for this.

First of all, thank you for developing the best free app for the ipod (One of the best free or not).
Many people probably already realize this, but you can find out what the PDB files in the search results are by clicking the result and then "read more about this molecule". That will present the webpage (without switching to safari) of the file. It is slightly more time consuming but gets the job done until the bug is fixed.

I really appreciate what you are doing. I found your app yesterday and was pretty amazed how well it is working. It is an amazing tool for protein-crytallographers. But it would be really nice, if you get it to work with shelx-res-files, so that small molecules can be handled with this app, too. And if you would even integrate orteps, I don't see a reason why every crystallographer, who has an iphone or an ipod touch wouldn't get your app instantly.

Thanks for the suggestions. I will add them to my list.

I would like to say that the program is amazing. I love the program, and I have not yet fully delved into all of its capability, I am sure. That said, I had posted in an older post (not seeing the newly created ones) about changing the rendering of the molecule's bond length, per the users input.

Also, would it be possible to add the ability to view structures in the .cml file format or even the .mol format? I know that protein crystallographers would not be the only ones to benefit, for I think many students/grad students/collaborators on computational chemistry research would also benefit (at least in terms of viewing optimized structures and the like). I think such an addition would increase the value of this program immensely.

Perhaps even view the output of ab inito computational programs, like GAMESS (which is an semi-open source, at least free program currently maintained by Mark Gordon's group at UIowa).

One thing I want to avoid is cluttering up the interface with too many options, but I'll take a look at maybe adding the adjustment you describe to a settings page as a preference for the application. For that setting, do you mean bond thickness? The bond length is set by the X,Y,Z coordinates of the centers of the respective atoms in the bond, values which are pulled from the PDB files themselves. I don't see how you'd adjust these lengths without altering the structures involved.

Support for many more file formats is in the works, as is the capability to easily sync structures to the application from the desktop, but I've been pulled away for the last few months by my new application. When that's released (hopefully within a month or so), I'll be able to turn my attention back to this. I'm committed to making this a useful educational / research tool, and I apologize for the slow progress as of late.

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