From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Wed Feb 27 2013 - 10:22:55 CST

Hello John,

I have removed the last column of the file and still see the same behaviour as shown below. There are 5070 fragments is is just about as many atoms in the system.

Is the structure analysis code looking at atom names, segid, or element names or a mixture of the three?

Brian

Info) Finished with coordinate file 000633/000633.complex.pdb.
Info) Analyzing structure ...
Info) Atoms: 5072
Info) Bonds: 5207
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 5070
Info) Waters: 0
Info) Segments: 130
Info) Fragments: 5070 Protein: 0 Nucleic: 0

________________________________________
From: John Stone [johns_at_ks.uiuc.edu]
Sent: Wednesday, February 27, 2013 8:18 AM
To: Bennion, Brian
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: definition of single word "protein" selection

Brian,
  The selection keywords "protein", "nucleic", and others, all
depend on the results of structure analysis code that runs when a
file is first loaded into VMD, or after the structure has been modified
and the "mol reanalyze ..." command is used. When you load the PDB
in question, what does VMD output in the console?, e.g.:

Info) Analyzing structure ...
Info) Atoms: 4309
Info) Bonds: 4158
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 766
Info) Waters: 254
Info) Segments: 1
Info) Fragments: 260 Protein: 4 Nucleic: 0

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 26, 2013 at 11:00:39PM +0000, Bennion, Brian wrote:
> Hello,
>
> I have a particular protein structure in the format of a pdb file that has
> been "touched" by a non-VMD program.
>
> If I load this pdb file into VMD and use a selection such as "not protein"
> I expect the protein structure to not be displayed. However it is still
> displayed.
>
> as described here "protein" is
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node89.html#5192
> a residue with atoms named, C, N CA, O
> The first few lines from my troublesome pdb file are shown and the
> requisite atoms exist.
> ATOM 1 N ASP P 5 35.879 3.155 17.581 0.00 0.00
> -0.066 N
> ATOM 2 HT1 ASP P 5 35.384 3.005 18.490 0.00 0.00
> 0.275 HD
> ATOM 3 HT2 ASP P 5 36.137 4.181 17.547 0.00 0.00
> 0.275 HD
> ATOM 4 HT3 ASP P 5 36.786 2.636 17.610 0.00 0.00
> 0.275 HD
> ATOM 5 CA ASP P 5 35.095 2.797 16.369 0.00 0.00
> 0.284 C
> ATOM 6 CB ASP P 5 36.101 2.881 15.193 0.00 0.00
> 0.155 C
> ATOM 7 CG ASP P 5 35.412 2.729 13.871 0.00 0.00
> 0.175 C
> ATOM 8 OD1 ASP P 5 35.607 1.678 13.207 0.00 0.00
> -0.648 OA
> ATOM 9 OD2 ASP P 5 34.660 3.650 13.453 0.00 0.00
> -0.648 OA
> ATOM 10 C ASP P 5 34.356 1.454 16.467 0.00 0.00
> 0.249 C
> ATOM 11 O ASP P 5 34.885 0.456 16.955 0.00 0.00
> -0.271 OA
> ATOM 12 N ALA P 6 33.078 1.392 16.025 0.00 0.00
> -0.346 N
>
> Brian

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