On Mon, Oct 24, 2005 at 10:18:40AM -0500, Kristl Adams wrote: > I have several txt files of coordinates (mostly heme type compounds) > that I'd like to format correctly for pymol to be able to read. I've > tried several things looking at PDBs with hemes, but can't figure it out. > > Will someone with more experience please show me how this should be > formatted for pymol to read properly.
You may have some luck doing a conversion using OpenBabel. http://openbabel.sourceforge.net http://packages.debian.org/openbabel For example, I took your file, saved it as TPP-NO.xyz and edited it to add the number of atoms as a first line (79) and then faked the last line by adding four zeros (0 0 0 0), then ran babel TPP-NO.xyz TPP-NO.pdb This generated a file that loaded the atoms into pymol, although the bonds are not depicted. That might be remedied by editing the CONECT records. What is the source of your coordinates? You may be able to save explicitly into a format that babel can convert to pdb without the need to edit it. -- Joe COMPND TPP-NO.xyz AUTHOR GENERATED BY OPEN BABEL 1.100.2 HETATM 1 Xx LIG 0 2.005 0.000 0.000 1.00 0.00 XX HETATM 2 Ca LIG 1 2.847 1.093 0.000 1.00 0.00 CA HETATM 3 Xx LIG 0 4.225 0.677 0.000 1.00 0.00 XX HETATM 4 Xx LIG 0 5.116 1.304 0.000 1.00 0.00 XX HETATM 5 Xx LIG 0 4.225 -0.679 -0.000 1.00 0.00 XX HETATM 6 Xx LIG 0 5.115 -1.307 -0.000 1.00 0.00 XX HETATM 7 Ca LIG 2 2.847 -1.094 -0.000 1.00 0.00 CA HETATM 8 Cm LIG 2 2.473 -2.475 -0.000 1.00 0.00 CM HETATM 9 Xx LIG 0 0.000 2.005 -0.000 1.00 0.00 XX HETATM 10 Ca LIG 3 -1.093 2.847 -0.000 1.00 0.00 CA HETATM 11 Xx LIG 0 -0.677 4.225 -0.000 1.00 0.00 XX HETATM 12 Xx LIG 0 -1.304 5.116 -0.000 1.00 0.00 XX HETATM 13 Xx LIG 0 0.679 4.225 0.000 1.00 0.00 XX HETATM 14 Xx LIG 0 1.307 5.115 0.000 1.00 0.00 XX HETATM 15 Ca LIG 1 1.093 2.848 0.000 1.00 0.00 CA HETATM 16 Cm LIG 1 2.473 2.474 0.000 1.00 0.00 CM HETATM 17 Xx LIG 0 -2.005 0.000 0.000 1.00 0.00 XX HETATM 18 Ca LIG 4 -2.847 -1.093 0.000 1.00 0.00 CA HETATM 19 Xx LIG 0 -4.225 -0.677 0.000 1.00 0.00 XX HETATM 20 Xx LIG 0 -5.116 -1.304 0.000 1.00 0.00 XX HETATM 21 Xx LIG 0 -4.225 0.679 -0.000 1.00 0.00 XX HETATM 22 Xx LIG 0 -5.115 1.307 -0.000 1.00 0.00 XX HETATM 23 Ca LIG 3 -2.847 1.093 -0.000 1.00 0.00 CA HETATM 24 Cm LIG 3 -2.472 2.474 -0.000 1.00 0.00 CM HETATM 25 Xx LIG 0 0.000 -2.005 -0.000 1.00 0.00 XX HETATM 26 Ca LIG 2 1.093 -2.849 -0.000 1.00 0.00 CA HETATM 27 Xx LIG 0 0.675 -4.226 -0.000 1.00 0.00 XX HETATM 28 Xx LIG 0 1.300 -5.119 -0.000 1.00 0.00 XX HETATM 29 Xx LIG 0 -0.681 -4.224 0.000 1.00 0.00 XX HETATM 30 Xx LIG 0 -1.311 -5.114 0.000 1.00 0.00 XX HETATM 31 Ca LIG 4 -1.093 -2.847 0.000 1.00 0.00 CA HETATM 32 Cm LIG 4 -2.473 -2.470 0.000 1.00 0.00 CM HETATM 33 Xx LIG 0 3.540 -3.542 0.000 1.00 0.00 XX HETATM 34 Xx LIG 0 4.028 -4.030 -1.195 1.00 0.00 XX HETATM 35 Xx LIG 0 3.643 -3.644 -2.139 1.00 0.00 XX HETATM 36 Xx LIG 0 5.004 -5.006 -1.195 1.00 0.00 XX HETATM 37 Xx LIG 0 5.389 -5.391 -2.139 1.00 0.00 XX HETATM 38 Xx LIG 0 5.492 -5.494 0.000 1.00 0.00 XX HETATM 39 Xx LIG 0 6.262 -6.264 0.000 1.00 0.00 XX HETATM 40 Xx LIG 0 5.004 -5.006 1.195 1.00 0.00 XX HETATM 41 Xx LIG 0 5.389 -5.391 2.139 1.00 0.00 XX HETATM 42 Xx LIG 0 4.028 -4.030 1.195 1.00 0.00 XX HETATM 43 Xx LIG 0 3.643 -3.644 2.139 1.00 0.00 XX HETATM 44 Xx LIG 0 3.540 3.541 0.000 1.00 0.00 XX HETATM 45 Xx LIG 0 4.028 4.029 -1.195 1.00 0.00 XX HETATM 46 Xx LIG 0 3.643 3.643 -2.139 1.00 0.00 XX HETATM 47 Xx LIG 0 5.004 5.005 -1.195 1.00 0.00 XX HETATM 48 Xx LIG 0 5.389 5.390 -2.139 1.00 0.00 XX HETATM 49 Xx LIG 0 5.492 5.492 0.000 1.00 0.00 XX HETATM 50 Xx LIG 0 6.262 6.263 0.000 1.00 0.00 XX HETATM 51 Xx LIG 0 5.004 5.005 1.195 1.00 0.00 XX HETATM 52 Xx LIG 0 5.389 5.390 2.139 1.00 0.00 XX HETATM 53 Xx LIG 0 4.028 4.029 1.195 1.00 0.00 XX HETATM 54 Xx LIG 0 3.643 3.643 2.139 1.00 0.00 XX HETATM 55 Xx LIG 0 -3.538 3.541 0.000 1.00 0.00 XX HETATM 56 Xx LIG 0 -4.026 4.030 -1.195 1.00 0.00 XX HETATM 57 Xx LIG 0 -3.641 3.644 -2.139 1.00 0.00 XX HETATM 58 Xx LIG 0 -5.001 5.006 -1.195 1.00 0.00 XX HETATM 59 Xx LIG 0 -5.386 5.392 -2.139 1.00 0.00 XX HETATM 60 Xx LIG 0 -5.488 5.494 0.000 1.00 0.00 XX HETATM 61 Xx LIG 0 -6.259 6.266 0.000 1.00 0.00 XX HETATM 62 Xx LIG 0 -5.001 5.006 1.195 1.00 0.00 XX HETATM 63 Xx LIG 0 -5.386 5.392 2.139 1.00 0.00 XX HETATM 64 Xx LIG 0 -4.026 4.030 1.195 1.00 0.00 XX HETATM 65 Xx LIG 0 -3.641 3.644 2.139 1.00 0.00 XX HETATM 66 Xx LIG 0 -3.542 -3.534 0.000 1.00 0.00 XX HETATM 67 Xx LIG 0 -4.032 -4.021 -1.195 1.00 0.00 XX HETATM 68 Xx LIG 0 -3.645 -3.637 -2.139 1.00 0.00 XX HETATM 69 Xx LIG 0 -5.010 -4.994 -1.195 1.00 0.00 XX HETATM 70 Xx LIG 0 -5.396 -5.379 -2.139 1.00 0.00 XX HETATM 71 Xx LIG 0 -5.499 -5.481 0.000 1.00 0.00 XX HETATM 72 Xx LIG 0 -6.271 -6.250 0.000 1.00 0.00 XX HETATM 73 Xx LIG 0 -5.010 -4.994 1.195 1.00 0.00 XX HETATM 74 Xx LIG 0 -5.396 -5.379 2.139 1.00 0.00 XX HETATM 75 Xx LIG 0 -4.032 -4.021 1.195 1.00 0.00 XX HETATM 76 Xx LIG 0 -3.645 -3.637 2.139 1.00 0.00 XX HETATM 77 N LIG 5 0.135 0.114 1.982 1.00 0.00 N HETATM 78 O LIG 5 0.661 0.554 2.899 1.00 0.00 O HETATM 79 Xx LIG 0 0.000 0.000 0.000 1.00 0.00 XX CONECT 1 CONECT 2 16 CONECT 3 CONECT 4 CONECT 5 CONECT 6 CONECT 7 8 CONECT 8 7 26 CONECT 9 CONECT 10 24 CONECT 11 CONECT 12 CONECT 13 CONECT 14 CONECT 15 16 CONECT 16 15 2 CONECT 17 CONECT 18 32 CONECT 19 CONECT 20 CONECT 21 CONECT 22 CONECT 23 24 CONECT 24 10 23 CONECT 25 CONECT 26 8 CONECT 27 CONECT 28 CONECT 29 CONECT 30 CONECT 31 32 CONECT 32 31 18 CONECT 33 CONECT 34 CONECT 35 CONECT 36 CONECT 37 CONECT 38 CONECT 39 CONECT 40 CONECT 41 CONECT 42 CONECT 43 CONECT 44 CONECT 45 CONECT 46 CONECT 47 CONECT 48 CONECT 49 CONECT 50 CONECT 51 CONECT 52 CONECT 53 CONECT 54 CONECT 55 CONECT 56 CONECT 57 CONECT 58 CONECT 59 CONECT 60 CONECT 61 CONECT 62 CONECT 63 CONECT 64 CONECT 65 CONECT 66 CONECT 67 CONECT 68 CONECT 69 CONECT 70 CONECT 71 CONECT 72 CONECT 73 CONECT 74 CONECT 75 CONECT 76 CONECT 77 78 CONECT 78 77 CONECT 79 MASTER 0 0 0 0 0 0 0 0 79 0 79 0 END
