compressed versus gzipped Re: Read compressed PDB files -question, suggestion
A thousand pardons. You are right. I phrased the question wrongly.
Chimera does open gzip'd files ( xx.gz). It does not open compress'd files (xx.Z).
You can also open gzipped files with Chimera's "open" command or as an argument as you start Chimera.
[...]
You can use the Chimera File / Open... dialog to directly open a gzip PDB file. This was added to Chimera about one year ago. It does not work
Why, you may ask, would anyone use compress these days ? If you mirror or rsync the protein data bank, they are still distributing files that have been squashed with compress and have a ".Z" extension. gunzip will happily eat and uncompress these files.
I do not know how chimera handles compressed files. If it reads from a pipe, it might be nice to persuade it to feed .Z files to gunzip. I think it might be more difficult if chimera uses the python/zlib interface.
Many thanks
On Dec 11, 2006, at 3:54 AM, Moo Cow wrote:
A thousand pardons. You are right. I phrased the question wrongly.
Chimera does open gzip'd files ( xx.gz). It does not open compress'd files (xx.Z).
Right. This is because Python's built-in gzip module can only uncompress '.gz' files and not '.Z' files. Since the gzip/uncompress programs aren't available on all platforms (and since .gz compression is considerably more popular than .Z compression) we hadn't bothered offering .Z decompression.
You can also open gzipped files with Chimera's "open" command or as an argument as you start Chimera.
[...]
You can use the Chimera File / Open... dialog to directly open a gzip PDB file. This was added to Chimera about one year ago. It does not work
Why, you may ask, would anyone use compress these days ? If you mirror or rsync the protein data bank, they are still distributing files that have been squashed with compress and have a ".Z" extension. gunzip will happily eat and uncompress these files.
I do not know how chimera handles compressed files. If it reads from a pipe, it might be nice to persuade it to feed .Z files to gunzip. I think it might be more difficult if chimera uses the python/zlib interface.
The underlying C++ code that handles PDB files needs a filename (this limitation is being worked on), so .Z decompression would have to go into a temporary file -- which is another reason we weren't motivated to offer it.
Here in our lab, we mirror the uncompressed PDB hierarchy, which obviously works fine with Chimera. It uses more bandwidth (though the biggest hit is when you initially set it up) and disk space, but is easier to work with for tools like 'grep' and custom programs.
I've added .Z decompression support to Chimera now. It is only enabled if Chimera can find a 'gzip' executable on your execution path (if it can't, it will say so in the Reply Log). I'll be sending you 3 files in a separate mail that should allow you to use your compressed PDB mirror. You will have to edit the pdbDir file to point to the mirror location as mentioned here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html .
--Eric
Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
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Eric Pettersen -
Moo Cow