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