Re: [Jmol-users] JSMOL load inline function

[Angel Herráez]

Glad you solved it

As far as I remember, the pipe character serves the same as your \n

Inline loading is  always tricky!



On 26 Sep 2016 at 12:49, Matthew Kennedy wrote:

Thank you Angel, in the end, it appears the issue was that it needs to print 
out the literal \n's 
in the script line. So the following worked for me: 

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Re: [Jmol-users] JSMOL load inline function

[Matthew Kennedy]

Thank you Angel, in the end, it appears the issue was that it needs to
print out the literal \n's in the script line.  So the following worked for
me:

script: 'load inline "25\n 0QURM735R7BTNZJNL\n C 1.417382 -0.002747
-0.016830 \n C -0.728040 1.261000 0.12 \n C -0.728040 -1.261000
0.12 \n C -0.000200 -0.001120 -2.476610 \n C 0.681964 -1.257343
-2.046422 \n C 0.689513 -1.259021 -0.497124 \n C 0.686920 1.252928
-2.043188 \n C 0.690974 1.255500 -0.494473 \n C -1.427655 0.001154
-1.993453 \n C -1.434070 0.000193 -0.439751 \n H 2.466351 -0.002875
-0.409649 \n H 1.469350 -0.003819 1.101986 \n H 1.239854 -2.171899
-0.149399 \n H 1.735616 -1.299560 -2.421564 \n H 0.138597 -2.159820
-2.424403 \n H 1.742916 1.290157 -2.412492 \n H 0.149834 2.159100 -2.421650
\n H 1.242744 2.167199 -0.145652 \n H -0.678726 -1.232324 1.214565 \n H
-1.282699 -2.176664 -0.217404 \n H -1.973196 -0.904100 -2.360988 \n H
-1.970618 0.909365 -2.357905 \n H -0.680052 1.233561 1.214680 \n H
-1.279960 2.177765 -0.219013 \n H -2.501775 0.000384 -0.098158 \n";'

In case anyone needs this in the future.

On Mon, Sep 26, 2016 at 12:29 PM, Angel Herráez 
wrote:

>
> You may also need a space between the pipe and the element symbol, so it
> seems
>
> > that lacks newline characters apparently. Jmol needs either those  or
> vertical
> > lines (the 'pipe' character, | ) Try inserting a pipe before each new
> line·
>
>
>
> 
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>



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404-376-0969
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Re: [Jmol-users] JSMOL load inline function

[Angel Herráez]

You may also need a space between the pipe and the element symbol, so it 
seems

> that lacks newline characters apparently. Jmol needs either those  or 
> vertical 
> lines (the 'pipe' character, | ) Try inserting a pipe before each new line·



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Re: [Jmol-users] JSMOL load inline function

[Angel Herráez]

Mathew,
that lacks newline characters apparently. Jmol needs either those  or vertical 
lines (the 'pipe' character, | ) Try inserting a pipe before each new line·
 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28871 Alcalá de Henares  (Madrid), Spain


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Re: [Jmol-users] JSMOL load inline function

[Matthew Kennedy]

Hi Angel,
  The script line is as follows:

script: 'load inline "25  0QURM735R7BTNZJNL  C 1.417382 -0.002747 -0.016830
 C -0.728040 1.261000 0.12  C -0.728040 -1.261000 0.12  C -0.000200
-0.001120 -2.476610  C 0.681964 -1.257343 -2.046422  C 0.689513 -1.259021
-0.497124  C 0.686920 1.252928 -2.043188  C 0.690974 1.255500 -0.494473  C
-1.427655 0.001154 -1.993453  C -1.434070 0.000193 -0.439751  H 2.466351
-0.002875 -0.409649  H 1.469350 -0.003819 1.101986  H 1.239854 -2.171899
-0.149399  H 1.735616 -1.299560 -2.421564  H 0.138597 -2.159820 -2.424403
 H 1.742916 1.290157 -2.412492  H 0.149834 2.159100 -2.421650  H 1.242744
2.167199 -0.145652  H -0.678726 -1.232324 1.214565  H -1.282699 -2.176664
-0.217404  H -1.973196 -0.904100 -2.360988  H -1.970618 0.909365 -2.357905
 H -0.680052 1.233561 1.214680  H -1.279960 2.177765 -0.219013  H -2.501775
0.000384 -0.098158 ";'

Thanks.

On Mon, Sep 26, 2016 at 12:06 PM, Angel Herráez 
wrote:

> Hi Mathew
>
> Possible sources of trouble (just a guess)
> - quotes (particularly when they get nested)
> - line breaks
>
> all that related to Javascript handling of your text string
>
> If you could provide a sample as plain text of what the php variable
> outputs.,
> it would help diagnosis.
>
> Another idea: write the output first to a , then load that value
> into
> JSmol (the browser will parse with less confilcts what is in the textarea
> in
> order to pass it along)
>
>
>
>
>
> 
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



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404-376-0969
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Re: [Jmol-users] JSMOL load inline function

[Angel Herráez]

Hi Mathew

Possible sources of trouble (just a guess)
- quotes (particularly when they get nested)
- line breaks

all that related to Javascript handling of your text string

If you could provide a sample as plain text of what the php variable outputs., 
it would help diagnosis.

Another idea: write the output first to a , then load that value into 
JSmol (the browser will parse with less confilcts what is in the textarea in 
order to pass it along)





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