#533 4B2Q - Load problems

open-fixed
Bob Hanson
5
2012-10-02
2012-10-02
Rolf Huehne
No

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" <<

Discussion

  • Bob Hanson
    Bob Hanson
    2012-10-02

    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.

     
  • Bob Hanson
    Bob Hanson
    2012-10-02

    • status: open --> open-fixed