Thank you, Chen Wenhan,
Looks like that was a bug from when the MOL2 reader was created years ago.
Should be fixed. See http://chemapps.stolaf.edu/jmol/Jmol-13.zip
Bob Hanson
On Sun, Mar 31, 2013 at 6:54 AM, 陈文瀚 <[email protected]> wrote:
> Hi,
>
> I met this problem that when I load a mol2 file into Jmol, the atoms named
> as CA was treated as calcium while I want it to be treated as carbon.
> the file content is like this :
> @<TRIPOS>MOLECULE
> *****
> 19 18 0 0 0
> SMALL
> GASTEIGER
>
> @<TRIPOS>ATOM
> 1 CA 2.5480 -0.6650 -0.0320 C.3 0 _NS0
> -0.0003
> 2 HA1 2.4580 -1.2420 -0.9510 H 0 _NS0
> 0.0847
> 3 HA2 2.5090 -1.3420 0.8220 H 0 _NS0
> 0.0847
> 4 N 3.9060 -0.0150 -0.0200 N.4 0 _NS0
> 0.2209
> 5 HT1 4.6470 -0.7050 -0.1970 H 0 _NS0
> 0.1995
> 6 HT2 4.1170 0.4070 0.8910 H 0 _NS0
> 0.1995
> 7 HT3 3.9960 0.6970 -0.7540 H 0 _NS0
> 0.1995
> 8 C4 1.4690 0.4060 0.0670 C.3 0 _NS0
> 0.1322
> 9 HC1 1.5610 0.9960 0.9830 H 0 _NS0
> 0.0752
> 10 HC2 1.4920 1.0810 -0.7940 H 0 _NS0
> 0.0752
> 11 O11 0.2260 -0.3190 0.0860 O.3 0 _NS0
> -0.4560
> 12 CA1 -0.8970 0.4310 0.0050 C.2 0 _NS0
> 0.3357
> 13 O15 -0.9070 1.6370 -0.0990 O.2 0 _NS0
> -0.2453
> 14 C1 -2.1220 -0.4160 0.0630 C.2 0 _NS0
> 0.0418
> 15 C15 -2.0380 -1.7160 0.2220 C.2 0 _NS0
> 0.0011
> 16 C6 -3.4780 0.2620 -0.0570 C.3 0 _NS0
> -0.0323
> 17 H61 -4.2930 -0.4650 -0.0230 H 0 _NS0
> 0.0280
> 18 H62 -3.5240 0.8040 -1.0070 H 0 _NS0
> 0.0280
> 19 H63 -3.6000 0.9730 0.7660 H 0 _NS0
> 0.0280
> @<TRIPOS>BOND
> 1 1 2 1
> 2 1 3 1
> 3 1 4 1
> 4 1 8 1
> 5 4 5 1
> 6 4 6 1
> 7 4 7 1
> 8 8 9 1
> 9 8 10 1
> 10 8 11 1
> 11 11 12 1
> 12 12 13 2
> 13 12 14 1
> 14 14 15 2
> 15 14 16 1
> 16 16 17 1
> 17 16 18 1
> 18 16 19 1
>
> The result from that is the atom CA and CA1 are painted as two large green
> calcium. I googled it and saw people mentioned set atomTypes. But it didn't
> work for me. The script would set up the atomType. However the
> interpretation of the atom is no based on this type(field 6 in the mol2
> file), but on the name of the atom (field 2). That causes for the ambiguity
> of CA as C or Calcium.
>
> Anyway, anyone know how to solve it?
>
> Cheers,
>
>
>
>
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>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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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Compete for recognition, cash, and the chance to get your game
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