Definitely some problems there. I think I know what's happening.
On Mon, Oct 22, 2012 at 8:46 AM, Rolf Huehne <[email protected]> wrote:
> On 10/19/2012 02:48 PM, Rolf Huehne wrote:
> > On 10/19/2012 02:33 PM, Robert Hanson wrote:
> >> Rolf,
> >>
> >> Are you looking for something more than
> >>
> >> try{
> >>
> >> } catch {
> >>
> >>
> >> }
> >>
> >> ?
> > No, I think that will be sufficient. I remembered having read about
> > something like this while following the 'Jmol-users' list but didn/t
> > remember it's name and didn't find it myself.
> >
> I tried it with Jmol.jar 13.1.7. With display and window it worked as
> expected. But when running it with the "-n" switch the script stopped
> and also didn't show my own error message:
>
> ===== With window (as expected) =================
> NOTE: loading 3021. file '/pdb_mirror/current/gz/au/pdb2qgp.ent.gz' with
> filter ':A'...
> ERROR: could NOT LOAD 3021. file
> '/pdb_mirror/current/gz/au/pdb2qgp.ent.gz' with filter ':A'
> /pdb_mirror/current/gz/au/pdb2qgp.ent.gz (No such file or directory)
> ----line 1 command 1 of try:
> load "/pdb_mirror/current/gz/au/pdb2qgp.ent.gz" 0 filter >>
> ":A" <<
> ----line 7 command 5 of function analysis_test:
> end
> ----line 3038 command 3022 of load_chains.scr:
> analysis_test ( "2qgp" , "A" , "3021" )
> STATUS: pdb_id='2qgp' chain='A' status='ERROR'
> ===================================================
>
> ===== Without window (script stops) ==================
> NOTE: loading 3021. file
> '/usr2/pollux/idb/pdb_mirror/current/gz/au/pdb2qgp.ent.gz' with filter
> ':A'...
>
>
> FileManager.getAtomSetCollectionFromFile(/usr2/pollux/idb/pdb_mirror/current/gz/au/pdb2qgp.ent.gz)
> FileManager opening
> /usr2/pollux/idb/pdb_mirror/current/gz/au/pdb2qgp.ent.gz
> file ERROR: /usr2/pollux/idb/pdb_mirror/current/gz/au/pdb2qgp.ent.gz
> /usr2/pollux/idb/pdb_mirror/current/gz/au/pdb2qgp.ent.gz (No such file
> or directory)
> Time for
> openFile(/usr2/pollux/idb/pdb_mirror/current/gz/au/pdb2qgp.ent.gz): 1 ms
> eval ERROR: /usr2/pollux/idb/pdb_mirror/current/gz/au/pdb2qgp.ent.gz (No
> such file or directory)
> ----line 1 command 1 of try:
> load
> "/usr2/pollux/idb/pdb_mirror/current/gz/au/pdb2qgp.ent.gz" 0 filter >>
> ":A" <<
> ----line 7 command 5 of function analysis_test:
> end
> ----line 3038 command 3022 of load_chains.scr:
> analysis_test ( "2qgp" , "A" , "3021" )
> ===================================================
>
> Below is shown my function and the first few function calls (I added the
> 'zap' just to be able to see a difference when calling it interactively
> with window):
>
> ====== Script (truncated) =========================
> function analysis_test (pdb_id,chain,counter) {
> zap;
> var filename = "/pdb_mirror/current/gz/au/pdb" + pdb_id + ".ent.gz";
> var chain_filter = ":" + chain;
> show @{"NOTE: loading " + counter + ". file '" + filename + "' with
> filter '" + chain_filter + "'..."};
> try {
> load @filename 0 FILTER @chain_filter;
> } catch(error_message) {
> show @{"ERROR: could NOT LOAD " + counter + ". file '" + filename +
> "' with filter '" + chain_filter + "'\n" + error_message};
> show @{"STATUS: pdb_id='" + pdb_id + "' chain='" + chain + "'
> status='ERROR'"};
> return "";
> }
> show @{"NOTE: file '" + filename + "' with filter '" +
> chain_filter + "' loaded successfully"};
> show @{"STATUS: pdb_id='" + pdb_id + "' chain='" + chain + "'
> status='OK'"};
> return "";
> }
> analysis_test("4axd","A","1")
> analysis_test("7odc","A","2")
> analysis_test("3swh","A","3")
> analysis_test("3ram","A","4")
> analysis_test("4eiu","A","5")
> ===================================================
>
> JmolData.jar also stops directly.
>
> But there was an additional problem with JmolData.jar. It didn't even
> reach file 3021 but stopped much earlier without any error message at
> all. It stopped for example sometimes at file 478 or sometimes at file
> 511 (upper limit until now).
> (COMMAND: java -Xmx5000m -jar JmolData.jar -ons load_chains.scr)
>
> I also noticed that within the "try/catch" part the "print" command (in
> contrast to the "show" command) apparantly didn't knew the variables
> "filename" and "chain_filter" if I declared them as local variables
> within the function (var filename = "xyz";).
>
> Regards,
> Rolf
>
> --
>
> Rolf Huehne
> Postdoc
>
> Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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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