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=3DSaveS... Best, Jon On 14 May 2013 18:37, Conrad Huang <conrad@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=23853897707157...>
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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