[Molvis-list] Models in pdb file

[Loren Williams]

This may not be entirely relevant but I have posted some scripts that 
generate (space) symmetry, using pymol.
Some of those scripts make animations. I did detect a few bugs in 
pymol, for example P61 makes a left handed screw.

They are posted here. 
http://web.chemistry.gatech.edu/~williams/xtal/visualization/index.html

Cheers,
Loren Williams
Georgia Tech

On Apr 14, 2005, at 4:28 AM, Inbal Tuvi-Arad wrote:

> 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
> __________________________________________
>
> _______________________________________________
> Molvis-list mailing list
> Molvis-list at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/molvis-list
>