Inserting the 26 seemingly innocuous lines listed below into the top of
a PDB file (my test case is 3hyd.pdb) causes it to fail to load in Jmol
14.3.12_2015.02.10 application (and also 14.2.12_2015.01.22). This is
important because these lines were generated by MolProbity when it
stripped the hydrogens out of a large PDB file and re-added the
hydrogens. The file downloaded from MolProbity has 406 USER lines at the
beginning and failed to load. I narrowed the problem down to something
about the 26 lines below. Strangely, the first 13 of these lines, the
last 13, or the middle 13 all work OK. Only when all 26 lines are
prepended to the test PDB file does it fail.
The failure is silent. It occurs with drag and drop, or File, Open. No
model appears, and 'select all' reports 0 atoms. I have not figured out
how to open the Java console in OS 10.10.2 Yosemite (Java 1.7.0_75).
Even tho in the Java Control Panel I have Advanced, Java Console, Show
console checked, I don't see the Java Console when I run Jmol.jar.
Here are the 26 lines:
USER MOD Single : S 61 SER OG : rot 160:sc= 0
USER MOD Single : T 1 PHE N :NH3+ 173:sc= 1.11 (180deg=1.07)
USER MOD Single : T 2 THR OG1 : rot 180:sc= -0.0466
USER MOD Single : T 25 SER OG : rot 79:sc= 0.741
USER MOD Single : T 30 LYS NZ :NH3+ 180:sc= 0 (180deg=0)
USER MOD Single : T 32 TYR OH : rot 180:sc= 0
USER MOD Single : T 33 ASN : amide:sc= -0.0444
K(o=-0.044,f=-1.4!)
USER MOD Single : T 34 SER OG : rot 171:sc= 0.665
USER MOD Single : T 37 SER OG : rot 87:sc= 0.122
USER MOD Single : T 38 SER OG : rot 76:sc= 0.945
USER MOD Single : T 42 ASN : amide:sc= 0.433 K(o=0.43,f=-0.32)
USER MOD Single : T 44 LYS NZ :NH3+ -165:sc= 1.15 (180deg=0.984)
USER MOD Single : T 45 THR OG1 : rot 92:sc= 0.812
USER MOD Single : T 49 SER OG : rot -23:sc= 0.868
USER MOD Single : T 55 GLN : amide:sc= 0 K(o=0,f=-0.78)
USER MOD Single : T 56 THR OG1 : rot -66:sc= 1.36
USER MOD Single : T 57 TYR OH : rot 180:sc= 0
USER MOD Single : T 61 SER OG : rot 160:sc= 0
USER MOD Single : U 1 PHE N :NH3+ 173:sc= 1.11 (180deg=1.08)
USER MOD Single : U 2 THR OG1 : rot 180:sc= -0.0415
USER MOD Single : U 25 SER OG : rot 79:sc= 0.74
USER MOD Single : U 30 LYS NZ :NH3+ 180:sc= 0 (180deg=0)
USER MOD Single : U 32 TYR OH : rot 180:sc= 0
USER MOD Single : U 33 ASN : amide:sc= -0.0327
K(o=-0.033,f=-1.2!)
USER MOD Single : U 34 SER OG : rot 170:sc= 0.661
USER MOD Single : U 37 SER OG : rot 86:sc= 0.122
Thanks for anyone's help, Eric
--
Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US
Martz.MolviZ.Org <http://Martz.MolviZ.Org>
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