Bob - thanks for the help.  I was running 11.2.14 and was encountering the issue I described, but when I used 11.5.9, it finally worked.  I may have a corrupt copy or there was an issue with version 11.2.14.

Thanks!
-Al


If we wanted to use the most recent "stable" version,

Bob Hanson wrote:
Al, what you are doing looks right to me. Hmm, I don't know. The 
following script worked for me in Jmol 11.5.9:

load data/1crn.pdb
set propertyAtomNumberField 1
set propertyDataField 2
x=load("atomData.dat")
select *
display *
data "property_score @x"
propertyColorScheme = "bwr"
color property_score


where atomData.dat is

 19 -1.038
 20 -1.038
 21 -1.038
 22 0.5235
 23 0.5235

When I instead select only atomno>20, then only three atoms are assigned 
the property. So that is working OK.

When you say "hangs" I have to ask more. Can you call up a Java console? 
Is it giving an error report of some sort by chance?

So I might need to see the files so I can try to reproduce that. You can 
send those directly to hansonr@stolaf.edu


Al Ramsey wrote:

  
Greetings - I'm hoping to get a suggestion on how I can troubleshoot a 
problem I'm facing regarding the loading of user data.  There are 
computed scores that were generated for each atom and I'd like to 
display as a color gradient.

Below is the script I am using.  I'm using the applet and it seems to 
hang at the last line... the console just says "pending" and just stays 
there:

#####
load "protein.pdb"
set propertyAtomNumberField 1
set propertyDataField 2

# The file "atomData.dat" is a two-column data file
# with the first column being the atom number and the
# second column being the data value, for example:
# 2519 -1.038
# 2520 -1.038
# 2521 -1.038
# 2522 0.5235
# 2523 0.5235
x=load("atomData.dat")
select :i   # data is for chain I
display :i  # display only chain I
data "property_score @x"
propertyColorScheme = "bwr"

# Jmol applet hangs at this line
color property_score

#####

Any advice on how I should troubleshoot would be greatly appreciated.

Thanks,
Al


 

    


  

-- 
Alvin Ramsey, PhD.
Senior Researcher/Senior Systems Architect
aramsey@vecna.com
703.998.5333
http://www.vecna.com

Vecna Technologies, Inc.
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Falls Church, VA  22041
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