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Dear Tamas, More than ten years ago, when I discovered Rasmol in the internet, since it is the default one, I have been using the pdb format as I learned it from the tutorials at the time. I know it has too many columns for different properties to be used by Rasmol, and most of them I don't even begin to understand, I still did not switch to xyz format, for instance, although it would suffice for my drawing purposes. As the time went on I gained some confidence, I deviated from the standards of the Rasmol world and started to use its properties for my own wishes, like the 'temperature' column, where I store the height of the atom from a chosen plane, so that when I look at it from the corresponding top view I can tell from the red to blue spectrum of the atoms that which are closer to the surface and which are deeper in the bulk of the crystal or amorphous slab. I use the CPK column differently also, since the colors of most atoms I work with are either purple (undefined) or close to each other (like in your version of perovskite all three atoms are similar tones of red). So I noticed that different letters in CPK column give different atom colors, same goes for the CHAIN column, but this time with a different set of color assignments. If my aim was to construct a macromolecule with lots of atoms and use the color codes arbitrarily and expose it to the public in the internet, that would have been out of standards and would have been ugly to see a H-atom making more than one bonds, for instance. Unfortunately, I could not think of sending my example pdb file (I should have called it "toy.pdb" instead of "perov.pdb" or "abo3.pdb") to this list is also exposing it to public, so I hope I am forgiven. It is such a toy file that even the lattice parameter is far from the real values, so that Rasmol does not bond the atoms and I would be in control which one to bond to which, or which bonds to show. All these unscientific discussion took me away from the "polyhedron" problem. Actually, for those who might be wandering about the solution within the Rasmol domain, I came up with a brute force solution, it is not a smart way in practice, but just to say it exists: Select all atoms on/within the polyhedron, spacefill off. Wireframe 0.05 or so. So we just have the polyhedron picture. Export as a gif. Import gif into xfig. Export as an eepic and edit it and compile it with latex. Find out which lines make up which triangle, isolate them as closed paths as "\path(1,2)(2,3)(3,1)". Insert "\shade\color{cyan}" in front of "\path(1,2)(2,3)(3,1)". Too much work. And this reminds me of another wishful thinking (of mine!), and since I don't know the mechanisms and structure of any of these above software, I dare to ask: Would it be possible technically Rasmol to export in "xfig" or "eepic" formats? Thanks for your time. Sinasi Tamas E. Gunda wrote: 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" <[EMAIL PROTECTED]> To: "Molecular Visualization, especially in education with freeware" <[EMAIL PROTECTED]> Sent: Saturday, February 12, 2005 12:39 PM Subject: Re: [Molvis-list] polygons |
