Thanks very much -- this is getting *more* confusing! If I add "set
debugScript; set loglevel 5;" to the script, nothing changes and the amount
of output to the console does not change (I only get "Script completed /
Jmol script terminated". However, the coordinates DO load, but no other
JMol commands in the script are executed, whether they are placed before or
after the "load" command. Now, if I cut and paste all of those commands
from the script file into the console, then every statement is executed!
So, I was suspecting the file itself, but I've also tried creating a
completely new file with a different name and got the same result....
I just tried something else & seem to have gotten it partially working. I
got rid of "zap;" and I changed:
select :Z;
center :Z;
to:
select *:Z;
center *:Z;
and now some additional commands are executing, but not all....I had
previously tried "center *;" and that didn't work either. Here is the full
script file (currently):
load FILES "protein.pdb" "ligand.pdb";
frames ALL;
select *:Z;
center *:Z;
zoom 300;
spacefill on;
delay 0.5;
zoom 100;
It is now getting as far as the first "zoom" - I can clearly observe that!
But, the spacefill is not applied, nor is the subsequent zoom-out. However,
if I paste all these commands into the console, all are executed
successfully!
Here is the output in the console window (from calling the script file via
an HTML link):
Eval.instructionDispatchLoop():1206556049237
Eval
pc:0
2 statements
----
Token[keyword(0x108010b) intValue=16(0x10) value="script"]
Token[string(0x4) value="load_script"]
----
Token[keyword(0x144) intValue=16(0x10) value="frame"]
Token[keyword(0x8000f) value="all"]
END
Token[keyword(0x108010b) intValue=16(0x10) value="script"] "load_script"
Eval.instructionDispatchLoop():1206556049241
Eval
pc:0
4 statements
----
Token[keyword(0x1081109) intValue=16(0x10) value="load"]
Token[identifier(0x1) value="files"]
Token[string(0x4) value="protein.pdb"]
Token[string(0x4) value="ligand.pdb"]
----
Token[keyword(0x31e) intValue=16(0x10) value="select"]
Token[keyword(0x80064) value="expressionBegin"]
Token[keyword(0x8001c) intValue=90(0x5a) value="spec_chain"]
Token[keyword(0x80065) value="expressionEnd"]
----
Token[keyword(0x304) intValue=16(0x10) value="center"]
Token[keyword(0x80064) value="expressionBegin"]
Token[keyword(0x8001c) intValue=90(0x5a) value="spec_chain"]
Token[keyword(0x80065) value="expressionEnd"]
----
Token[keyword(0x152f) intValue=16(0x10) value="zoom"]
Token[integer(0x2) intValue=300(0x12c) value="300"]
END
Token[keyword(0x1081109) intValue=16(0x10) value="load"] files "protein.pdb"
"ligand.pdb"
Successfully loaded:files
select *:Z
Token[keyword(0x304) intValue=16(0x10) value="center"] *:Z
Token[keyword(0x152f) intValue=16(0x10) value="zoom"] 300
Token[keyword(0x144) intValue=16(0x10) value="frame"] Token[keyword(0x8000f)
value="all"]
Script completed
Jmol script terminated
So, it looks to me like it is simply ignoring the last three statements, but
I can't figure out why!
Thanks for your interest!
-Tom
On Tue, Mar 25, 2008 at 4:37 PM, Angel Herráez <[EMAIL PROTECTED]> wrote:
> Hi, Thomas, welcome to Jmol world!
>
> I can see no reason for the problem you describe.
> Try these:
>
> 1.- open the Java console* and see if there is some error there
> (*find a coffee cup icon in the taskbar, bottom right of your screen,
> right-click on it,
> choose "Open Console")
>
> 2.- open Jmol console from the applet pop-up menu and try commands from
> there,
> both your "script load.script" and any other commands after that, like
> "spacefill off".
> See if they work and if any errors show up there or in the Java console.
>
>
>
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