As it was suggested, I'd like to use the PDB format file instead of the XYZ
format file. However, my information about PDB is not good. I wrote two
simple following frames:
Frame 1
ATOM 1 Fe ASN 1 19.058 16.247 11.361 1.00 0.000
ATOM 2 Na ASN 1 16.367 1.038 19.679 1.00 0.000
END
FRAME 2
ATOM 1 Fe ASN 1 20.058 16.247 11.361 1.00 0.000
ATOM 2 Na ASN 1 15.367 1.138 19.679 1.00 0.000
END
But Jmol couldn't separate the two frames. Can somebody tell me what I've
missed there? and introduce a good link about how to write simple PDBs.
Thanks,
Behrooz
At 05:35 PM 8/30/2005, Miguel wrote:
> Dear All,
>
> I'm very novice in using JMOL. I want to model defects (like vacancies or
> interstitials) in SiC, using the XYZ file format. I defined VC for a
> carbon-vacancy.
Jmol expects the XYZ format to contain element symbols.
You cannot define your own element symbol.
> My question is what the command is in JMOL to select VC,
> and for example to change its color. The command in Rasmol is "select
> *.VC?".
I am surprised ... I did not know that RasMol could do this with an XYZ file.
> But this command doesn't work in Jmol.
>
> Does anybody know the appropriate command?
Jmol will never recognize element type VC.
Anything unrecognized gets mapped to the element name 'unknown' (or
'dummy') whos element symbol is Xx.
Alternatively, if you store your data as a PDB file then you can make the
atom name VC and it will work just like you described above
select *.VC?
Miguel
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