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 HerrŠez <angel.herraez@uah.es> 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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