[Molvis-list] (and JMol) polygons

Tamas E. Gunda tgunda at puma.unideb.hu
Sun Feb 13 04:44:40 EST 2005


I don't know what software created this pdb file of perovskit, but it has
many mistakes and different other programs may behave oddly. HETATM should
be instead of ATOM (small bug), the CONECT records are incomplete (all bonds
should be there twice, A-->B and B-->A), elemental symbols are in the column
of  residue names and vice versa, the residue names are in the column of
atom names (big bugs). According to the recent PDB spefications in columns
77 and 78 the elemental symbol should be present in order to avoid
confusions when unusual atom names are tried to translate to elemental
symbols.

It should like for example:

HEADER    perovskite
COMPND    perovskite
SOURCE    e-mail
SOURCE    Created by Mol2Mol 5.4
SOURCE    10:22:01, Sunday, Feb 13, 2005
HETATM    1 Ti   o       1       8.000   8.000   8.000  1.00  0.00
Ti
HETATM    2  O2  s       2       8.000   8.000   4.000  1.00  0.00
O
HETATM    3  O3  s       2       8.000   4.000   8.000  1.00  0.00
O
HETATM    4  O4  s       2       4.000   8.000   8.000  1.00  0.00
O
HETATM    5  O5  s       2      12.000   8.000   8.000  1.00  0.00
O
HETATM    6  O6  s       2       8.000  12.000   8.000  1.00  0.00
O
HETATM    7  O7  s       2       8.000   8.000  12.000  1.00  0.00
O
HETATM    8 Sr8  d       3       4.000   4.000   4.000  1.00  0.00
Sr
HETATM    9 Sr9  d       3      12.000   4.000   4.000  1.00  0.00
Sr
HETATM   10 Sr10 d       3       4.000  12.000   4.000  1.00  0.00
Sr
HETATM   11 Sr11 d       3      12.000  12.000   4.000  1.00  0.00
Sr
HETATM   12 Sr12 d       3       4.000   4.000  12.000  1.00  0.00
Sr
HETATM   13 Sr13 d       3      12.000   4.000  12.000  1.00  0.00
Sr
HETATM   14 Sr14 d       3       4.000  12.000  12.000  1.00  0.00
Sr
HETATM   15 Sr15 d       3      12.000  12.000  12.000  1.00  0.00
Sr
CONECT    2    3    4    5    6
CONECT    3    2    4    5    7
CONECT    4    2    3    6    7
CONECT    5    2    3    6    7
CONECT    6    2    4    5    7
CONECT    7    3    4    5    6
END

Dr. Tamas E. Gunda
Dept. of Pharmaceutical Chemistry
University of Debrecen
POBox 36
H-4010 Debrecen, Hungary

tgunda (.AT.) puma.unideb.hu

----- Original Message ----- 
From: "Sinasi Ellialtioglu" <sinasi at metu.edu.tr>
To: "Molecular Visualization, especially in education with freeware"
<molvis-list at bioinformatics.org>
Sent: Saturday, February 12, 2005 12:39 PM
Subject: Re: [Molvis-list] polygons


> Dear Miguel, Abhijit, and Inbal,
>
> I thank you all for your comments and guidiance.
> With all I know about Rasmol I can obtain octahedra but I don't know a
> way to make its
> surfaces as solid or semi-transparent. I enclose a simple case of a
> perovskite pdb file, and
> a script file to be implemented afterwards:
>
> abo3.pdb
>
> ATOM      1  o   Ti  d   2       8.000   8.000   8.000      1  24.00
> ATOM      2  s   O   b   3       8.000   8.000   4.000      1  60.00
> ATOM      3  s   O   b   3       8.000   4.000   8.000      1  48.00
> ATOM      4  s   O   b   3       4.000   8.000   8.000      1  36.00
> ATOM      5  s   O   c   3      12.000   8.000   8.000      1  36.00
> ATOM      6  s   O   c   3       8.000  12.000   8.000      1  48.00
> ATOM      7  s   O   c   3       8.000   8.000  12.000      1  60.00
> ATOM      8  d   Sr  a   1       4.000   4.000   4.000      1  12.00
> ATOM      9  d   Sr  a   1      12.000   4.000   4.000      1  12.00
> ATOM     10  d   Sr  a   1       4.000  12.000   4.000      1  12.00
> ATOM     11  d   Sr  a   1      12.000  12.000   4.000      1  12.00
> ATOM     12  d   Sr  a   1       4.000   4.000  12.000      1  12.00
> ATOM     13  d   Sr  a   1      12.000   4.000  12.000      1  12.00
> ATOM     14  d   Sr  a   1       4.000  12.000  12.000      1  12.00
> ATOM     15  d   Sr  g   1      12.000  12.000  12.000      1  12.00
> TER
> #CONECT    1    2    3    4    5    0    0
> #CONECT    6    1    0    0    0    0    0
> #CONECT    7    1    0    0    0    0    0
> #
> CONECT    2    3    4    5    6    0    0
> CONECT    7    3    4    5    6    0    0
> CONECT    6    4    5    0    0    0    0
> CONECT    3    4    5    0    0    0    0
>
> and abo3.spt
>
> set ambient 60
> background white
> set boundbox on
> color boundbox black
> spacefill 0.45
> wireframe 0.15
> color atoms cpk
> rotate y 15
> rotate x -15
> select 3
> spacefill 0.10
> wireframe 0.01
>
> If I had only a way to shade a closed surface bounded by CONECT'ed
lines....
> Anyway, I will visit JMOL solution since it is already there.
>
> Thank you all again.
> Sinasi
>
> Miguel wrote:
>
> >>Hi everybody,
> >>
> >>I am a Rasmol user, and since this list is now bringing together a
> >>multi-software society
> >>I would like to ask if drawing polygons around oxygen octahedra or
> >>tetrahedra in various
> >>crystal structures (like in YBCO) is possible in any of Rasmol, Jmol,
> >>Chime, Protein Explorer, or else.
> >>
> >>
> >
> >I have recently added rendering of polyhedrons (tetrahedrons and
> >octahedrons) to Jmol. They can be rendered as solid or translucent.
> >
> >The code has not yet been officially released, but is currently in
> >prerelease test phase.
> >
> >There is not much documentation either, but there are only a few commands
> >and it is pretty straightforward.
> >
> >Check out www.jmol.org
> >
> >Download the prerelease version from sourceforge at:
> >
> >http://sourceforge.net/project/showfiles.php?group_id=23629
> >
> >Then you can post specific questions on the jmol-users list. Sign up at
> >www.jmol.org/lists
> >
> >
> >Miguel
> >
> >_______________________________________________
> >Molvis-list mailing list
> >Molvis-list at bioinformatics.org
> >https://bioinformatics.org/mailman/listinfo/molvis-list
> >
> >
> >
> _______________________________________________
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