pdb file format help?

[tt6681_theresat]

I tried a google search but can't find anything useful...so maybe one of you knows

Comments

[petefred]

Not sure if one can get excel to output a fixed width format (blame the fortran people for PDBs looking like that

[petefred]

(oops, I started writing that and forgot that you said tab-delimited; replacing awk -F "," with awk -F "\t" will work for a tab delimited file.

[tt6681_theresat]

Ok, that *almost* works... unfortunately I'm not at all familiar with the code to fix it (but hey, at least now I can navigate to the right folders and stuff on command line... I might be learning slowly but I am learning)... it returns the first line of my file in the perfect format...but just the first line.
Any ideas?

(I just exported it as a .csv and used the first option)

[petefred]

Hm, can you just email me the file or post the first couple lines? I'm not sure what "the first option" is -- don't have excel.

[caethan]

This python incantation should work as well:
http://pastebin.com/uvWadxU7

Just save that to a file named convert.py and run
> python convert.py
at the command line (assuming you have python installed, which should be the case if you're running on a mac).

[tt6681_theresat]

ok, just tried that and got this http://pastebin.com/bjwGxgdx

[caethan]

Whoops, had mismatched quotes. Try this:

http://pastebin.com/7VM7ipJv

[petefred]

You'll need to explicitly convert all the fields to appropriate types to make '%' happy with that, I think... or just make everything a string.