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 <kristl@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


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--

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