[Chimera-users] Error during PDB Fetch

Eric Pettersen pett at cgl.ucsf.edu
Tue Oct 27 16:51:08 PDT 2009

Hi Bryan,
	In the past we had seen this error on Linux when there was a mismatch  
(32-bit vs. 64-bit) between the system libraries and Chimera.  For  
some reason that mismatch causes Python's call to gethostbyname (to  
resolve 'www.rcsb.org') to fail.  There doesn't seem to be a mismatch  
in your case.
	What we would like you to do is install the 64-bit 1.3 release and  
see if that works.  Depending on whether it does or not would  
determine what we would do next.
	As a (horrible) workaround for your problem with the 1.4 release you  
would edit a couple of files in the distribution and change every  
instance of 'www.rcsb.org' with ''.  The files are in  
<your Chimera distribution>/share/chimera and are named __init__.py  
and fetch.py.  Let me know if that doesn't solve the problem.

                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Oct 26, 2009, at 7:02 PM, Bryan Krantz wrote:

> Dear Chimera Users:
> Does anyone know how to resolve this bug. I tried to load a PDB file  
> from the web using the ID 3hvd.
> Got this error back:
> Error reading 3hvd:
> Error during PDB fetch: [Errno socket error] (-2, 'Name or service  
> not known')
> I am running this Chimera :
> Linux 64-bit	chimera-1.4-linux_x86_64.exe
> Size: 77850528 bytes
> MD5: 1e05f4607699c88467e81cc249aa4ad1
> My OS is Debian Lenny AMD64.
> Thanks in advance for your help.
> Yours,
> bryan
> -- 
> Bryan Krantz
> University of California, Berkeley
> Department of Molecular & Cell Biology
> Department of Chemistry
> 476 Stanley Hall #3220
> Berkeley, CA 94720-3220
> Phone: (510) 666-2788
> Email: bakrantz at berkeley.edu
> Lab: 492 Stanley Hall
> Lab phone: (510) 666-2789
> URL: http://mcb.berkeley.edu/labs/krantz/
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