<div dir="ltr"><div style>Hi Conrad,</div><div style><br></div><div style>I guess that was a bad link for me to post and something has expired. This link should give the required file:</div><a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=71739&disopt=3DSaveSDF">http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=71739&disopt=3DSaveSDF</a><br>
<div><br></div><div style>Best,</div><div style><br></div><div style>Jon</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 14 May 2013 18:37, Conrad Huang <span dir="ltr"><<a href="mailto:conrad@cgl.ucsf.edu" target="_blank">conrad@cgl.ucsf.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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.<br>
<br>
Conrad<div><div class="h5"><br>
<br>
On 5/14/2013 1:19 AM, Jon Fuller wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
I tried to read an SDF file directly downloaded from pubchem into<br>
Chimera. However, I ran into the following problem (link to example file<br>
used, and reply log below). Is this expected behaviour, or a bug?<br>
<br>
Additionally I tried to import the pubchem CID 71739 (same compound)<br>
from the fetch structure by ID tab, and got the error message:<br>
Unexpected end of file (parser state: counts) in MOL/SDF file 'FILEPATH<br>
HERE!'<br>
<br>
Many thanks in advance,<br>
<br>
Jon<br>
<br>
<a href="http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=crtvw&reqid=238538977071577164" target="_blank">http://pubchem.ncbi.nlm.nih.<u></u>gov/vw3d/vw3d.cgi?cmd=crtvw&<u></u>reqid=238538977071577164</a><br>
<br>
You are now running Chimera version 1.8 (build 38642).<br>
Your previous version was 1.5 (build 32133).<br>
Check the release notes for new features and other info.<br>
(To access the release notes, use the Help menu to bring up the User's<br>
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Then click the 'Documentation index' link and you will then see a link<br>
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Error while processing CID_71739_1183b00000003_conf.<u></u>sdf:<br>
Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data<br>
<br>
Error reading CID_71739_1183b00000003_conf.<u></u>sdf:<br>
Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data<br>
<br>
Error reading CID_3672_e5800000001_conf.sdf:<br>
Non-numeric charge (1 -0.65) in PUBCHEM_MMFF94_PARTIAL_CHARGES data<br>
<br>
Error reading CID_71739_1183b00000003_conf.<u></u>sdf:<br>
Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data<br>
<br>
<br></div></div>
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</blockquote>
</blockquote></div><br></div>