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 <kri...@physics.purdue.edu> 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 > PyMOL-users@lists.sourceforge.net > 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
