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 [EMAIL PROTECTED]
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
>
>
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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