[Chimera-users] Error reading PubChem3D SDF Files

[Jon Fuller]

Hi Conrad,

I guess that was a bad link for me to post and something has expired. This
link should give the required file:
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=71739&disopt=3DSaveSDF

Best,

Jon


On 14 May 2013 18:37, Conrad Huang <conrad at cgl.ucsf.edu> wrote:

> 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<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
>>
>>
>> ______________________________**_________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/**mailman/listinfo/chimera-users<http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20130514/bbd222b2/attachment.html>