Currently Jmol requires one of the following sanctioned PDB headers within
the first 16 lines:
private final static String[] pdbLineStartRecords = {
"Pdb", "HEADER", "OBSLTE", "TITLE ", "CAVEAT", "COMPND", "SOURCE",
"KEYWDS",
"EXPDTA", "AUTHOR", "REVDAT", "SPRSDE", "JRNL ", "REMARK ",
"DBREF ", "SEQADV", "SEQRES", "MODRES",
"HELIX ", "SHEET ", "TURN ",
"CRYST1", "ORIGX1", "ORIGX2", "ORIGX3", "SCALE1", "SCALE2", "SCALE3",
"ATOM ", "HETATM", "MODEL ", "LINK ",
};
"USER" is not among those
On Tue, Feb 10, 2015 at 10:59 PM, Eric Martz <ema...@microbio.umass.edu>
wrote:
> 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
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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