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,
------------------------------------------------------------------------------
Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete
for recognition, cash, and the chance to get your game on Steam.
$5K grand prize plus 10 genre and skill prizes. Submit your demo
by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
