[Chimera-users] compressed versus gzipped Re: Read compressed PDB files -question, suggestion

Eric Pettersen pett at cgl.ucsf.edu
Tue Dec 12 16:51:40 PST 2006

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 Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

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