Bugs item #3573830, was opened at 2012-10-02 09:10 Message generated for change (Settings changed) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3573830&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: File Input/Output Group: None Status: Open >Resolution: Fixed Priority: 5 Private: No Submitted By: Rolf Huehne (rhuehne) Assigned to: Bob Hanson (hansonr) Summary: 4B2Q - Load problems Initial Comment: Newer versions of Jmol than 11.6.8 have problems loading the asymmetric unit file of PDB entry 4B2Q (Java 1.6.0_35 on Linux). Jmol 11.6.8 loads the structure just fine (see http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=1deh). Jmol 11.8.8 takes about an hour and at least 7 GB of RAM just to tell "no atoms loaded". Jmol 12.2.2 takes several minutes and 1.7 GB of RAM and just displays a few amino acids (see http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=4b2q&JMOLVERSION=12.2.2). Jmol 13.1.4 needs several minutes and the displays the following error message: script ERROR: Error reading file at line 72414: HETATM70077 C2 ATP A1511 140.665 74.194 236.670 1.00 68.34 C Premature EOF for file http://www.imb-jena.de/cgi-bin/idb_send.pl?CODE=4B2Q&MODE=compressed-asymmetricSNP type Pdb ----line 1 command 4 of http://www.imb-jena.de/ImgLibPDB/tmp/4B2Q_snp.pdb.asymmetric.default-3813.jmz: load >> "http://www.imb-jena.de/cgi-bin/idb_send.pl?CODE=4B2Q&MODE=compressed-asymmetricSNP"; << ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2012-10-02 10:01 Message: Thanks. yes, that's a poorly created REMARK 350. Fix is at http://chemapps.stolaf.edu/jmol/Jmol-13.zip Will be part of the next release of 13.0.6 and 13.1.6 as well. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3573830&group_id=23629 ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
