Re: [Jmol-users] Loading User Data

[Al R. <ar...@ve...>]

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 ha...@st...
>
>
> 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
ar...@ve...
703.998.5333
http://www.vecna.com

Vecna Technologies, Inc.
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Falls Church, VA  22041
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f: 703.998.5816


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