[Chimera-users] Error reading PubChem3D SDF Files

[Eric Pettersen]

Hi Jon,
	I do get the error with the downloaded SDF, but if I fetch directly in Chimera it works fine for me.  I tried your compound (71739) and the example compound (12123).  The difference is possibly that Chimera's fetch goes through an intermediate web service (Pub3D, described in Chimera's Fetch By ID help page) that undoubtedly doesn't contain the problematic section of the SDF file.
	How about you try the direct fetch again, but check the "Ignore any cached data" button at the bottom of the fetch dialog and see what happens.
	In the interim, I will try to get Chimera to handle the downloaded version also.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu


On May 14, 2013, at 1:19 AM, Jon Fuller <jonathan.fuller at gmail.com> 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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