[Molvis-list] Models in pdb file

Thu Apr 14 10:28:00 EDT 2005

Dear Inval,

There are other programs that do the kind of problem you are trying to solve
see: http://kinemage.biochem.duke.edu/, where they have examples of it.
Also using PyMol (DeLano Scientific) at http://www.delanoscientific.com/ I
think you would be able to use pdb's to do your modelling as you wish:  Here
you can make a sequence of all the structures with their changes and then
play them as a morph (see http://molmovdb.mbb.yale.edu/cgi-bin/movie.cgi). I
must warn you I am not an expert at all, thus "at your own risk" but the
programmes I mention are available free of charge.

Cordially,

Ricardo A. Correa C.
Molecular Biology Amateur

-----Original Message-----
From: molvis-list-bounces+trans.lab=skynet.be at bioinformatics.org
[mailto:molvis-list-bounces+trans.lab=skynet.be at bioinformatics.org] On
Behalf Of Inbal Tuvi-Arad
Sent: 14 April 2005 10:28
To: 'Molecular Visualization, especially in education with freeware'
Subject: [Molvis-list] Models in pdb file

Dear Colleagues,
  We are trying to create pdb files of small inorganic molecules with
several models.  We encounter problems in the way Chime presents these
files.  If any of you could help us we will be very grateful.  Our purpose
is to create a Website that calculates the distance of a molecule from the
symmetry of its point group.  For that we would like to present the original
molecule and its perfectly symmetric match with a small animation.

I will try to describe the problem.  We take a simple small molecule (e.g.
SF6), draw it and save it as pdb file.  So far, Chime presents it as it
should.  We duplicate the model in the file, and add the model/endmdl tags
to separate the models.  We then change a bit one of the coordinates (of one
of the atoms), that is, we distort one of the molecules, so we can see the
difference between them.  When we present this file in Chime, the
connectivity is different then it should be, even though each model for
itself is perfectly all right.  We built a special script that allows us to
separate models on the screen with buttons.  We know this script is working
because we tested it with a model that works.  Even without this special
script, Chime should present the molecule as if there is one extra atom
which is misplaced.  Is there a problem with our pdb files or with the way
Chime presents such files?  Is there any other format that can be used to
save more then one model of a molecule in a file?

Here is the file we created for SF6:

COMPND

MODEL 01
HETATM    1  F   UNK     0       0.001   1.080   0.001
HETATM    2  F   UNK     0      -0.001  -1.080  -0.000
HETATM    3  F   UNK     0      -1.080   0.000  -0.000
HETATM    4  F   UNK     0       1.080   0.000  -0.000
HETATM    5  F   UNK     0      -0.001   0.000   1.080
HETATM    6  F   UNK     0       0.001  -0.001  -1.080
HETATM    7  S   UNK     0       0.000   0.000  -0.000
CONECT    7    1    2    3    4                              
CONECT    7    5    6                                        
CONECT    1    7                                             
CONECT    2    7                                             
CONECT    3    7                                             
CONECT    4    7                                             
CONECT    5    7                                             
CONECT    6    7                                             
ENDMDL
MODEL 02
HETATM    1  F   UNK     0       1.000   1.080   0.000
HETATM    2  F   UNK     0      -0.000  -1.080  -0.000
HETATM    3  F   UNK     0      -1.080   0.000  -0.000
HETATM    4  F   UNK     0       1.080  -0.000   0.000
HETATM    5  F   UNK     0      -0.000   0.000   1.080
HETATM    6  F   UNK     0       0.000  -0.000  -1.080
HETATM    7  S   UNK     0       0.000   0.000   0.000
CONECT    7    1    2    3    4                              
CONECT    7    5    6                                        
CONECT    1    7                                             
CONECT    2    7                                             
CONECT    3    7                                             
CONECT    4    7                                             
CONECT    5    7                                             
CONECT    6    7                                             
ENDMDL
END

Sincerely,
Inbal

__________________________________________
Dr. Inbal Tuvi-Arad
Department of Natural Sciences
The Open University of Israel
108 Ravutski St., POB 808,
Raanana, 43107, Israel
Tel: 972-9-778-1773
Fax: 972-9-778-0661
Email: inbaltu at openu.ac.il
__________________________________________

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