VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 27 2013 - 10:28:52 CST

Brian,
  The fact that you're getting nearly as many residues as atoms is
an immediate cause for concern, IMHO. VMD uses a combination of the
atom names and bond structure to classify parts of the structure.
The fact that you're getting so many residues likely indicates that
one or more of your atom names is something VMD completely fails to
recognize. If you can set the atom names to match the PDB naming scheme,
it should cure this problem. You can of course keep that atom "type"
field set to anything you want, as this is ignored by the structure analysis
code in VMD. So, if you want to be able to refer to your original naming
scheme, you could assign the original names to the "type" field, and
then map your atom names to match the PDB naming scheme. That would be
my first suggestion. If you are able to send me your structure, I would
be happy to take a quick look at it.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Feb 27, 2013 at 04:22:55PM +0000, Bennion, Brian wrote:
> 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
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078