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[Jmol-users] How to save a JMol script - still not solved
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From: Reinhold S. <rs...@un...> - 2011-07-08 11:37:14
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> Having 3 different molecules in one JMol window, and after arranging
> them interactively to give the best representation of what I want to
> show, I stumbled upon the problem how to save this interactively
> generated script (on Windows Vista + Firefox 4.01 + JMol 12.0.39, if
> that matters).
>
> Using the
> File - Save script with state
> gives me the generated script in the JMol console and also in the java
> console.
>
> But I am unable to copy anything via CTRL-A, CTRL-C, CTRL-V into any
> editor program outside Java.
> Also it seems the consoles don't give me the option do save their
> contents ...
>
> So I' stuck (I dont want to copy the script by typing it symbol for
> symbol; it is quite long).
>
> Can anybody help?
>
> THanks
> Reinhold
>
I asked here above questions about a month ago, but unfortunately due to
lots of other work I had to do recently, I was unable to try out the
suggested solutions up to now.
1. Suggestion:
Using the signed applet
(
jmolInitialize("jmol/",true);
instead of
jmolInitialize("jmol/");
)
did not change anything. By the way I'm developing on localhost. So
there should be no issues with accessing URLs from anywhere else.
2. Suggestion (Angel Herráez)
Drag and drop the script from the jmol console to an editor (instead of
using CTRL-A, CTRL-C, CTRL-V)
does not work either. I always get the symbol that drag and drop is not
allowed
(no matter what editor I use, Windows Vista, JMol 12.0.39, Sun/Oracle
Java 1.6.0_25)
> Sorry to rescue this thread so late, but I found a fix.
>
> I've just found that, similar to what was described for MacOS, the cure for this limitation in
> Windows is to select the text in the Jmol script console and (rather than trying to copy it,
> which cannot be pasted outside Java) drag the selected text to a text editor.
> So, no need to open the Java console and copy from there. Just have a text editor at hand
> when you need to copy text that has been output to the Jmol script console.
>
> (Tested on WinXP, Sun/Oracle Java 1.6.0_25, Jmol 12.0.x)
Now I CAN copy Information from the JAVA console to an editor.
Unfortunately the Java console does not refelct all jmol commands,
especially the commands with coordinates are truncated:
> DATA "coord set"
> 119 ;
> Jmol Property Data Format 1 -- Jmol 12.0.39 2011-02-04 07:47;
> 1 C [LLW]0:A.C/1.1_#1 15.808979 12.575748 -1.9898928 ;
> 2 O [ZZZ]4:A.O/1.1_#2 1.9772998 18.798574 3.0733123 ;
> 3 C [LLW]0:A.C/1.1_#3 2.1830313 18.56621 1.7326368 ;
> 4 O [ZZZ]4:A.O/1.1_#4 1.6255851 19.29174 0.9535861 ;
> 5 N [LCW]446:A.N/1.1_#5 10.964918 14.905299 -2.3756077 ;
> 6 C [LCL]404:A.C/1.1_#6 9.894557 15.80536 -2.6844807 ;
> 7 C [LCL]404:A.C/1.1_#7 9.918614 16.426691 -3.9531403 ;
> 8 C [LCL]404:A.C/1.1_#8 8.856955 17.250237 -4.32592 ;
> 9 C [LCL]404:A.C/1.1_#9 7.7651854 17.454082 -3.4797227 ;
> 10 C [LCL]404:A.C/1.1_#10 7.762911 16.836826 -2.2138665 ;
> 11 C [LCL]404:A.C/1.1_#11 8.836377 16.036463 -1.7961241 ;
> 12 N [LCW]446:A.N/1.1_#12 6.5946965 16.979734 -1.3948852 ;
> 13 C [LLW]0:A.C/1.1_#13 6.5694203 16.79647 0.005976353 ;
> 14 O [ZZZ]446:A.O/1.1_#14 7.562506 16.774021 0.6928738 ;
> 15 C [LCL]404:A.C/1.1_#15 4.343219 17.670307 0.8542317 ;
> 16 C [LCL]404:A.C/1.1_#16 5.1769786 16.593086 0.5421457 ;
> 17 C [LCL]404:A.C/1.1_#17 4.7619824 15.277666 0.7813227 ;
> 18 C [LCL]404:A.C/1.1_#18 3.486769 15.038955 1.3139714 ;
> 19 C [LCL]404:A.C/1.1_#19 2.6473434 16.10605 1.6443704 ;
> 20 C [LCL]404:A.C/1.1_#20 3.0840995 17.417067 1.4142116 ;
> 21 C [LLW]0:A.C/1.1_#21 3.1124983 13.60282 1.5624653 ;
> 22 O [ZZZ]446:A.O/1.1_#22 3.803285 12.852937 2.214505 ;
> 23 N [LCW]446:A.N/1.1_#23 1.9148092 13.206674 0.92680573 ;
> 24 C [LCL]404:A.C/1.1_#24 1.4568963 11.855642 0.79157126 ;
> 25 C [LCL]404:A.C/1.1_#25 2.155736 10.77515 1.3444179 ;
> 26 C [LCL]404:A.C/1.1_#26 1.7208419 9.471325 1.0618236 ;
> 27 C [LCL]404:A.C/1.1_#27 0.56360507 9.242073 0.2919804 ;
> 28 C [LCL]404:A.C/1.1_#28 -0.14572828 10.338749 -0.20132324 ;
> 29 C [LCL]404:A.C/1.1_#29 0.28872105 11.644202 0.02622952 ;
> 30 N [LCW]446:A.N/1.1_#30 2.493695 8.337667 1.4737875 ;
> 31 C [LLW]0:A.C/1.1_#31 3.4159856 8.338484 2.5471625 ;
> 32 O [ZZZ]446:A.O/1.1_#32 3.4338934 9.187774 3.4046805 ;
> 33 C [LCL]404:A.C/1.1_#33 5.60258 7.4225307 1.8080117 ;
> 34 C [LCL]404:A.C/1.1_#34
> Trace message truncated for length over 10K
Only the Jmol console give the whole set of coordinates for my molecules.
So how I'm I supposed to get those new coordinates to disk?
(Making screenshots, saving them as jpg and submitting the 20-40 jpgs to
an OCR program?
There must be an easier way)
Greetings
Reinhold
------------------------------------------------------------------------------------------
Dr. Reinhold Störmann
University of Bremen - Center for Environmental Research and Sustainable
Technology
Leobener Str.
D-28359 Bremen
Germany
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