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From: Kristl A. <kr...@ph...> - 2005-10-24 15:24:10
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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. Thanks! This is one of the files: (This is a heme type molecule, TPP-NO) FE 0.000000 0.000000 0.300000 N1 2.005000 0.000000 0.000000 CA1 2.847000 1.093360 0.000000 CB1 4.224580 0.677440 0.000000 HB1 5.116370 1.304200 0.000000 CB2 4.224580 -0.678560 -0.000000 HB2 5.115270 -1.306870 -0.000000 CA2 2.847000 -1.094470 -0.000000 CM1 2.473030 -2.474910 -0.000000 N2 0.000000 2.005000 -0.000000 CA3 -1.093360 2.847000 -0.000000 CB3 -0.677440 4.224580 -0.000000 HB3 -1.304200 5.116370 -0.000000 CB4 0.678560 4.224580 0.000000 HB4 1.306870 5.115270 0.000000 CA4 1.092590 2.847770 0.000000 CM2 2.473030 2.473800 0.000000 N3 -2.005000 0.000000 0.000000 CA5 -2.847000 -1.093360 0.000000 CB5 -4.224580 -0.677440 0.000000 HB5 -5.116370 -1.304200 0.000000 CB6 -4.224580 0.678560 -0.000000 HB6 -5.115270 1.306870 -0.000000 CA6 -2.847000 1.093360 -0.000000 CM3 -2.472040 2.473520 -0.000000 N4 0.000000 -2.005000 -0.000000 CA7 1.092590 -2.848880 -0.000000 CB7 0.674720 -4.225870 -0.000000 HB7 1.300210 -5.118550 -0.000000 CB8 -0.681280 -4.223950 0.000000 HB8 -1.310860 -5.113740 0.000000 CA8 -1.093360 -2.847000 0.000000 CM4 -2.472890 -2.469800 0.000000 C1 3.540060 -3.541940 0.000000 C12 4.027960 -4.029840 -1.195110 H12 3.642590 -3.644470 -2.139080 C13 5.003770 -5.005650 -1.195110 H13 5.389140 -5.391020 -2.139080 C14 5.491670 -5.493550 0.000000 H14 6.262420 -6.264300 0.000000 C15 5.003770 -5.005650 1.195120 H15 5.389140 -5.391020 2.139080 C16 4.027960 -4.029840 1.195120 H16 3.642590 -3.644470 2.139080 C2 3.540050 3.540820 0.000000 C22 4.027960 4.028730 -1.195120 H22 3.642580 3.643350 -2.139080 C23 5.003770 5.004540 -1.195120 H23 5.389140 5.389910 -2.139080 C24 5.491670 5.492440 0.000000 H24 6.262420 6.263190 0.000000 C25 5.003770 5.004540 1.195110 H25 5.389140 5.389910 2.139080 C26 4.027960 4.028730 1.195110 H26 3.642590 3.643350 2.139080 C3 -3.538280 3.541340 0.000000 C32 -4.025820 4.029600 -1.195120 H32 -3.640730 3.643940 -2.139080 C33 -5.000900 5.006130 -1.195120 H33 -5.385990 5.391790 -2.139080 C34 -5.488440 5.494400 0.000000 H34 -6.258620 6.265720 0.000000 C35 -5.000900 5.006130 1.195110 H35 -5.385990 5.391790 2.139080 C36 -4.025820 4.029600 1.195110 H36 -3.640730 3.643940 2.139080 C4 -3.542500 -3.534230 0.000000 C42 -4.031590 -4.020950 -1.195110 H42 -3.645280 -3.636510 -2.139080 C43 -5.009760 -4.994380 -1.195110 H43 -5.396070 -5.378820 -2.139080 C44 -5.498850 -5.481100 0.000000 H44 -6.271460 -6.249970 0.000000 C45 -5.009760 -4.994380 1.195120 H45 -5.396070 -5.378820 2.139080 C46 -4.031590 -4.020950 1.195120 H46 -3.645280 -3.636510 2.139080 N 0.135400 0.113610 1.981740 O 0.660820 0.554490 2.898570 |
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From: Tsjerk W. <ts...@gm...> - 2005-10-24 15:48:38
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Hi Kristl, The pdb-file is column formatted. You can find a specification of the file format at http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html The easiest is to write a python script to do the conversion. Hope it helps, Tsjerk On 10/24/05, Kristl Adams <kr...@ph...> 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. > > Thanks! > > This is one of the files: (This is a heme type molecule, TPP-NO) > > FE 0.000000 0.000000 0.300000 > N1 2.005000 0.000000 0.000000 > CA1 2.847000 1.093360 0.000000 > CB1 4.224580 0.677440 0.000000 > HB1 5.116370 1.304200 0.000000 > CB2 4.224580 -0.678560 -0.000000 > HB2 5.115270 -1.306870 -0.000000 > CA2 2.847000 -1.094470 -0.000000 > CM1 2.473030 -2.474910 -0.000000 > N2 0.000000 2.005000 -0.000000 > CA3 -1.093360 2.847000 -0.000000 > CB3 -0.677440 4.224580 -0.000000 > HB3 -1.304200 5.116370 -0.000000 > CB4 0.678560 4.224580 0.000000 > HB4 1.306870 5.115270 0.000000 > CA4 1.092590 2.847770 0.000000 > CM2 2.473030 2.473800 0.000000 > N3 -2.005000 0.000000 0.000000 > CA5 -2.847000 -1.093360 0.000000 > CB5 -4.224580 -0.677440 0.000000 > HB5 -5.116370 -1.304200 0.000000 > CB6 -4.224580 0.678560 -0.000000 > HB6 -5.115270 1.306870 -0.000000 > CA6 -2.847000 1.093360 -0.000000 > CM3 -2.472040 2.473520 -0.000000 > N4 0.000000 -2.005000 -0.000000 > CA7 1.092590 -2.848880 -0.000000 > CB7 0.674720 -4.225870 -0.000000 > HB7 1.300210 -5.118550 -0.000000 > CB8 -0.681280 -4.223950 0.000000 > HB8 -1.310860 -5.113740 0.000000 > CA8 -1.093360 -2.847000 0.000000 > CM4 -2.472890 -2.469800 0.000000 > C1 3.540060 -3.541940 0.000000 > C12 4.027960 -4.029840 -1.195110 > H12 3.642590 -3.644470 -2.139080 > C13 5.003770 -5.005650 -1.195110 > H13 5.389140 -5.391020 -2.139080 > C14 5.491670 -5.493550 0.000000 > H14 6.262420 -6.264300 0.000000 > C15 5.003770 -5.005650 1.195120 > H15 5.389140 -5.391020 2.139080 > C16 4.027960 -4.029840 1.195120 > H16 3.642590 -3.644470 2.139080 > C2 3.540050 3.540820 0.000000 > C22 4.027960 4.028730 -1.195120 > H22 3.642580 3.643350 -2.139080 > C23 5.003770 5.004540 -1.195120 > H23 5.389140 5.389910 -2.139080 > C24 5.491670 5.492440 0.000000 > H24 6.262420 6.263190 0.000000 > C25 5.003770 5.004540 1.195110 > H25 5.389140 5.389910 2.139080 > C26 4.027960 4.028730 1.195110 > H26 3.642590 3.643350 2.139080 > C3 -3.538280 3.541340 0.000000 > C32 -4.025820 4.029600 -1.195120 > H32 -3.640730 3.643940 -2.139080 > C33 -5.000900 5.006130 -1.195120 > H33 -5.385990 5.391790 -2.139080 > C34 -5.488440 5.494400 0.000000 > H34 -6.258620 6.265720 0.000000 > C35 -5.000900 5.006130 1.195110 > H35 -5.385990 5.391790 2.139080 > C36 -4.025820 4.029600 1.195110 > H36 -3.640730 3.643940 2.139080 > C4 -3.542500 -3.534230 0.000000 > C42 -4.031590 -4.020950 -1.195110 > H42 -3.645280 -3.636510 -2.139080 > C43 -5.009760 -4.994380 -1.195110 > H43 -5.396070 -5.378820 -2.139080 > C44 -5.498850 -5.481100 0.000000 > H44 -6.271460 -6.249970 0.000000 > C45 -5.009760 -4.994380 1.195120 > H45 -5.396070 -5.378820 2.139080 > C46 -4.031590 -4.020950 1.195120 > H46 -3.645280 -3.636510 2.139080 > N 0.135400 0.113610 1.981740 > O 0.660820 0.554490 2.898570 > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. > Get Certified Today * Register for a JBoss Training Course > Free Certification Exam for All Training Attendees Through End of 2005 > Visit http://www.jboss.com/services/certification for more information > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 |
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From: D. J. A. <de...@ia...> - 2005-10-25 14:35:38
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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 |
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