Angel Herraez wrote:
>> Can you think of anything inside jmol that helps me to visualize this
>> "abstract" superposition mapping?
>
> On a first thought, there may be many wasy to indicate that: csame
> color, lines between matching atoms, etc.
>
> The key point is
> how and where is your "assignment (superposition)" indicated?
>
> Please, provide details and an example file
okay I attached three sources.
[1] source file ind sdf format
[2] target file in sdf format
and a mapping.
the mapping looks like:
[ MAP ] 1:16 2:15 3:10 4:14 5:9 6:11 7:13 8:12
where 1:16 means atom one from file [1] corresponds to atom 16 in file
[2] and so on.
okay to be clear - I do not expect JMol to do more than it is intended
for - but maybe there is a functionality built-in Jmol that can help us
here to visualize that. maybe a jmol script...
many thanks in advance...
raphael
[1]
1
SItclserve07250621173D 0 0.00000 0.000001
15 15 0 0 0 0 0 0 0 0999 V2000
1.8890 1.7851 -0.0009 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7730 0.7724 -0.0022 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0858 -0.6712 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5031 1.1816 0.0003 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2422 -1.0420 0.0024 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.0081 -1.6639 -0.0002 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5969 0.1889 -0.0004 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2842 -1.2547 -0.0029 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.7534 0.5597 0.0023 O 0 0 0 0 0 0 0 0 0 0 0 0
1.4675 2.7903 -0.0028 H 0 0 0 0 0 0 0 0 0 0 0 0
2.5015 1.6497 0.8905 H 0 0 0 0 0 0 0 0 0 0 0 0
2.5052 1.6479 -0.8894 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.7317 2.2371 0.0033 H 0 0 0 0 0 0 0 0 0 0 0 0
0.2206 -2.7194 0.0013 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.0840 -1.9805 -0.0034 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
2 4 2 0 0 0 0
3 5 2 0 0 0 0
3 6 1 0 0 0 0
4 7 1 0 0 0 0
6 8 2 0 0 0 0
7 9 2 0 0 0 0
7 8 1 0 0 0 0
1 10 1 0 0 0 0
1 11 1 0 0 0 0
1 12 1 0 0 0 0
4 13 1 0 0 0 0
6 14 1 0 0 0 0
8 15 1 0 0 0 0
M END
[2]
2
SItclserve07250621173D 0 0.00000 0.000001
28 31 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0800 0.3600 -1.3600 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2000 -0.0800 -2.0800 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4000 0.3000 -3.7000 S 0 0 0 0 0 0 0 0 0 0 0 0
-2.8800 -0.5600 -3.6600 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.1400 -0.9600 -4.7000 S 0 0 0 0 0 0 0 0 0 0 0 0
-5.4400 -2.0400 -3.5200 S 0 0 0 0 0 0 0 0 0 0 0 0
-6.7000 -2.4400 -4.5600 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.6400 -3.1800 -3.8400 N 0 0 0 0 0 0 0 0 0 0 0 0
-8.7200 -3.5600 -4.6000 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.8400 -4.3000 -4.2200 C 0 0 0 0 0 0 0 0 0 0 0 0
-10.8000 -4.5600 -5.2200 C 0 0 0 0 0 0 0 0 0 0 0 0
-10.6400 -4.0800 -6.5400 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.4800 -3.3400 -6.8800 C 0 0 0 0 0 0 0 0 0 0 0 0
-8.5200 -3.0800 -5.8800 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.1400 -2.2200 -6.2200 S 0 0 0 0 0 0 0 0 0 0 0 0
-3.1600 -1.0800 -2.4000 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.2000 -0.8000 -1.4600 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1400 -1.1800 -0.1000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0200 -0.7600 0.6200 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8484 0.3073 0.5750 H 0 0 0 0 0 0 0 0 0 0 0 0
0.6844 0.9465 -1.8254 H 0 0 0 0 0 0 0 0 0 0 0 0
-9.9647 -4.6534 -3.2178 H 0 0 0 0 0 0 0 0 0 0 0 0
-11.6691 -5.1336 -4.9740 H 0 0 0 0 0 0 0 0 0 0 0 0
-11.3901 -4.2742 -7.2780 H 0 0 0 0 0 0 0 0 0 0 0 0
-9.3350 -2.9845 -7.8787 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9147 -1.7609 0.3553 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.9317 -1.0164 1.6551 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
7 8 1 0 0 0 0
8 9 2 0 0 0 0
9 10 1 0 0 0 0
10 11 2 0 0 0 0
11 12 1 0 0 0 0
12 13 2 0 0 0 0
13 14 1 0 0 0 0
14 15 2 0 0 0 0
10 15 1 0 0 0 0
15 16 1 0 0 0 0
8 16 1 0 0 0 0
5 17 2 0 0 0 0
17 18 1 0 0 0 0
3 18 2 0 0 0 0
18 19 1 0 0 0 0
19 20 2 0 0 0 0
1 20 1 0 0 0 0
1 21 1 0 0 0 0
2 22 1 0 0 0 0
11 23 1 0 0 0 0
12 24 1 0 0 0 0
13 25 1 0 0 0 0
14 26 1 0 0 0 0
19 27 1 0 0 0 0
20 28 1 0 0 0 0
M END
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