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.


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
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

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 

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
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.





Alvin Ramsey, PhD.
Senior Researcher/Senior Systems Architect

Vecna Technologies, Inc.
5205 Leesburg Pike, Suite 210
Falls Church, VA  22041
t: 703.998.5333
f: 703.998.5816

Better Technology, Better World (TM)

The contents of this message may be privileged and confidential. Therefore, if this message has been received in error, please delete it without reading it. Your receipt of this message is not intended to waive any applicable privilege. Please do not disseminate this message without the permission of the author.