<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">The next release candidate and daily builds will handle the new format for charges that PubChem is using. This only affects files directly downloaded from PubChem and then opened in Chimera. Files fetched by Chimera directly don't have a charges section and therefore work and continue to work. It seems that the intermediate web service (Pub3D) may have been down when you reported the problem initially -- it seems to be up now.<div><br></div><div>--Eric</div><div><br></div><div><br></div><div><br><div><div>On May 15, 2013, at 2:21 PM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Jon,<div><span class="Apple-tab-span" style="white-space:pre"> </span>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.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>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.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>In the interim, I will try to get Chimera to handle the downloaded version also.</div><div><br></div><div>--Eric</div><div><br> Eric Pettersen<br> UCSF Computer Graphics Lab<br> <a href="http://www.cgl.ucsf.edu/">http://www.cgl.ucsf.edu</a><br><br></div><div><br><div><div>On May 14, 2013, at 1:19 AM, Jon Fuller <<a href="mailto:jonathan.fuller@gmail.com">jonathan.fuller@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><div style="">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?</div>
<div style=""><br></div><div style="">Additionally I tried to import the pubchem CID 71739 (same compound) from the fetch structure by ID tab, and got the error message:</div><div style="">Unexpected end of file (parser state: counts) in MOL/SDF file 'FILEPATH HERE!'</div>
<div style=""><br></div><div style="">Many thanks in advance,</div><div style=""><br></div><div style="">Jon</div><div><br></div><a href="http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=crtvw&reqid=238538977071577164" target="_blank" style="font-family:arial,sans-serif;font-size:13px">http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=crtvw&reqid=238538977071577164</a><br style="font-family:arial,sans-serif;font-size:13px">
<br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px">You are now running Chimera version 1.8 (build 38642).</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px">Your previous version was 1.5 (build 32133).</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px">Check the release notes for new features and other info.</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px">(To access the release notes, use the Help menu to bring up the User's Guide.</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px">Then click the 'Documentation index' link and you will then see a link</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px">for the release notes.)</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px">Error while processing CID_71739_1183b00000003_conf.</span><span style="font-family:arial,sans-serif;font-size:13px">sdf:</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px">Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data</span><br style="font-family:arial,sans-serif;font-size:13px"><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px">Error reading CID_71739_1183b00000003_conf.</span><span style="font-family:arial,sans-serif;font-size:13px">sdf:</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px">Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data</span><br style="font-family:arial,sans-serif;font-size:13px"><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px">Error reading CID_3672_e5800000001_conf.sdf:</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px">Non-numeric charge (1 -0.65) in PUBCHEM_MMFF94_PARTIAL_CHARGES data</span><br style="font-family:arial,sans-serif;font-size:13px">
<br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px">Error reading CID_71739_1183b00000003_conf.</span><span style="font-family:arial,sans-serif;font-size:13px">sdf:</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px">Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data</span><br></div>
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