Trouble uploading custom pdb file
Fri, 11/21/2008 - 11:30
Hi: I have been trying to upload a custom pdb file and everything does well, except that there are no atoms loaded. I just tried downloading a pdb from the RCSB site, posting it on a website, and then trying to upload. This failed as well. I therefore assume it is some format/program issue about how I am saving the .pdb file on my Mac. By default it saves them as PyMol file, but I also tried saving it in Word as a text file. Any thoughts of what might be going on?
Thanks for any help you can give.
Sun, 11/23/2008 - 12:49
#2
The web site with the pdb file I am trying to load is:
Mon, 11/24/2008 - 00:03
#3
I'm getting a 404 error (file not found) when I try to access that link. Could you double-check the address to make sure that the file is indeed there?
Tue, 11/25/2008 - 12:49
#4
I figured out the problem with help from a friend. The file needs to be a .gz. I gizpped it and it uploaded perfectly.
Sat, 12/06/2008 - 16:05
#5
Hi: I thought Molecules would be a fun opportunity to carry around my molecules on the iPhone but I'm having problems with my custom molecules, downloaded from my iDisk. The downloading process itself works fine and the new files appear correctly in the registry of Molecules. However, the program sees no atoms (Statistics / Number of Atoms 0), both in the case of a .pdb or .pdb.gz format. The same files may be opened with e.g. Mercury or CrystalMaker. Any help will be greatly appreciated.
Sat, 12/06/2008 - 17:33
#6
Have you tried this with a standard .pdb.gz file, such as one downloaded from the RCSB Protein Data Bank? I haven't had a chance to try out iDisk downloading, so I'd like to see if it's the structures themselves or the iDisk service causing the problems. I just got back from a conference, but I'll give this a try when I get settled back in.
It sounds like the file is not being properly parsed. I've seen this where a web server was gzipping the text file before sending, although I should be detecting that and unzipping it on the device end properly.
To help debug this, could you post the link where you've placed this file? I could enable some debug flags and see what's actually being downloaded.
Another thing you could try is to download the iPhone Backup Extractor from here: http://supercrazyawesome.com/ . Sync your iPhone after downloading the problematic PDB file, then use the Backup Extractor to grab Molecule's files. One of the files in the Documents directory of Molecules should be this PDB file. If it's the text PDB file, try opening it using a text editor and see if the text is clean or garbled. If it's gzipped, something's not being detected properly and I'll need to account for that.