Thanks, Bob. It solves the problem.
If this is fine, I will just use this version.
Regards,
Wenhan
_________________________________
Wenhan Chen
School of Chemistry and Molecular Biosciences
The University of Queensland
2013/4/1 Robert Hanson <[email protected]>
> 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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