[Chimera-users] Error reading PubChem3D SDF Files

Conrad Huang conrad at cgl.ucsf.edu
Tue May 14 09:37:40 PDT 2013


Hmm.  The link below returns a page with the error message "invalid 
input type".  Going to the PubChem/Pub3D URL returns a page with the 
error message "Not Found [MAIN PAGE]".  Perhaps there's something going 
on with the PubChem server?  I'll try checking on it again later.

Conrad

On 5/14/2013 1:19 AM, Jon Fuller wrote:
> I tried to read an SDF file directly downloaded from pubchem into
> Chimera. However, I ran into the following problem (link to example file
> used, and reply log below). Is this expected behaviour, or a bug?
>
> Additionally I tried to import the pubchem CID 71739 (same compound)
> from the fetch structure by ID tab, and got the error message:
> Unexpected end of file (parser state: counts) in MOL/SDF file 'FILEPATH
> HERE!'
>
> Many thanks in advance,
>
> Jon
>
> http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=crtvw&reqid=238538977071577164
>
> You are now running Chimera version 1.8 (build 38642).
> Your previous version was 1.5 (build 32133).
> Check the release notes for new features and other info.
> (To access the release notes, use the Help menu to bring up the User's
> Guide.
> Then click the 'Documentation index' link and you will then see a link
> for the release notes.)
> Error while processing CID_71739_1183b00000003_conf.sdf:
> Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
>
> Error reading CID_71739_1183b00000003_conf.sdf:
> Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
>
> Error reading CID_3672_e5800000001_conf.sdf:
> Non-numeric charge (1 -0.65) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
>
> Error reading CID_71739_1183b00000003_conf.sdf:
> Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
>
>
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