Thanks, Bob. USER is not a sanctioned PDB format record type, but rather
something that MolProbity is doing. I confirm that adding a single line
containing only "REMARK " at the top of the indigestible file renders it
OK with Jmol. I will contact David Richardson about this.
Eric
On 2/11/15 7:40 AM, Robert Hanson wrote:
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 <mailto: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 <http://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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