Feature Requests item #1539636, was opened at 2006-08-13 13:34
Message generated for change (Comment added) made by hansonr
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>Category: None
Group: None
Status: Open
Priority: 5
Submitted By: Eric Martz (emartz)
>Assigned to: Bob Hanson (hansonr)
Summary: "show pdbheader" stops prematurely
Initial Comment:
There appears to be a bug in "show pdbheader" (Jmol
applet 10.2.0). In my tests, it shows from the start
of the PDB file to the last REMARK line. In fact, the
header continues beyond what is being shown, ending
with the last line preceding a line beginning with any
one of three record types:
ATOM
HETATM
MODEL
Presently I am using "show pdbheader" via
messageCallback to obtain the results of a ConSurf
run, which are inserted in the pdb file header in
lines beginning "!". Such lines are ignored by other
programs that use PDB files, to the best of my
knowledge. Since the ConSurf lines are inserted at the
beginning of the header, this works OK.
Later, however, I envision using the SEQRES lines to
generate an interactive sequence display in
FirstGlance in Jmol. Although SEQRES is part of the
header, it is not currently being messaged by "show
pdbheader" due to the bug. Therefore I would
appreciate this bug being fixed.
Thanks, -Eric Martz
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>Comment By: Bob Hanson (hansonr)
Date: 2006-08-13 15:51
Message:
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Actually, Jmol was set to accept a number of other record
types as closure to the header, including "ATOM ", "HELIX
", "SHEET ", "TURN ", "MODEL ", "SCALE", "HETATM",
"SEQRES", and "DBREF "
But I agree that many of these could be useful and so have
modified 10.x.41 to only recognize "ATOM ", "MODEL ", and
"HETATM" as header-closures.
Also, 10.x.41 corrects a bug that did not allow for the
preferred method of obtaining this information:
var info=jmolGetPropertyAsString("fileHeader")
Thus, no callbacks are necessary, and the information is
returned synchronously. (The web page waits for the return
information before continuing.)
If Jmol-new.js is not being used, then the equivalent is:
var info=applet.getPropertyAsString("fileheader")+""
(The added "" converts the function return from a Java
string to a JavaScript string.)
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