[Proteopedia] Script compiler error

[Karl Oberholser]

Eran & others,
The commands that I used are: Select :c, :n; isosurface minset 1000 pocket
cavity 1.2.  I am doing everything in Proteopedia.
 
Here is a message that Angel sent to me after he did some testing.
 
"I've run your script and the error says
script compiler ERROR: } expected
 
but I'm not sure about the the use of the colon, n:m syntax. In any case,
since it's a state 
produced by Jmol, I think it's a bug. You should report it to
jmol-developers
Though I guess what Bob will tell you... upgrade!
 
If I load the pdb file and try the offending line in 11.6.13, there is no
error"
It appears that upgrading Jmol will help.
 
Karl



>>> Eran Hodis <eran.hodis at weizmann.ac.il> 1/16/2009 7:28 PM >>>
Hi Karl and Angel,

What is the command, Karl, that you issued in order to make and display the
surface in the SAT (Proteopedia's Scene Authoring Tools)?

The generated state script that you referenced has the following line:
  "calculate surfaceDistance WITHIN ({6073:9161 23278:26366 35260:35345
35430:35515}) ;"

which I cannot successfully execute on its own.  I get the same error as
you:
"script compiler ERROR: } expected"

Karl I assume the answer to Angel's question is that you used only the Jmol
applets on the Proteopedia website?  If so, we currently run 11.5.51,
although we should update it when we have a chance.

Best,
Eran

-----Original Message-----
>From Karl Oberholser <oberhols at messiah.edu>
Sent Fri 1/16/2009 5:51 PM
To proteopedialist-for-users at bioinformatics.org 
Subject [Proteopedia] Script compiler error

Hi All,

I am attempting to compute a surface using the Jmol cavity command.  I can
make and display the surface in SAT, but when I test the green link no
surface is made, and I obtain the following error:
script compiler ERROR: } expected
----line 199 command 22 of
/wiki/scripts/Complex_III_of_Electron_Transport_Chain/Surface_qn/2.spt:
         calculate surfaceDistance WITHIN ({6073:9161 23278:26366
35260:35345 35430:35515}) ; <<<<
----line 1 command 2 of  file null:
         script >>
"/wiki/scripts/Complex_III_of_Electron_Transport_Chain/Surface_qn/2.spt"
<<
I do not know what to make of this!  Any help would be appreciated.

Karl



Karl M. Oberholser 
Professor Chemistry
Chemistry & Biochemistry Dept.    
Messiah College 
Grantham, PA  US 
Molecular Science Lab:
http://www.messiah.edu/molscilab/ 
Proteopedia user page: 
http://proteopedia.org/wiki/index.php/User:Karl_Oberholser                

    
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