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I want to create a 3D molecular file using coordinates taken from:

Here are the coordinates:

              X             Y            Z
C(1)          0.5419        0.1631       0.7095
C(2)          0.4579        0.2047       0.5345
C(3)          0.3080        0.1713       0.5168
C(4)          0.2903        0.0286       0.5727
C(5)          0.3950        0.0004       0.7409
C(6)          0.3870        0.1080       0.8678
C(7)          0.4858        0.2192       0.8450
C(8)          0.1028        0.2512       0.3219
C(9)          0.0323        0.2713       0.1411
C(10)         0.0857        0.2213       0.0238
C(11)         0.0189        0.2435       -0.1419
C(12)        -0.0995        0.3166        -0.1875
C(13)        -0.1528        0.3671      -0.0719
C(14)        -0.0880        0.3462      0.0951
C(15)         0.5172        0.1331      0.4127
C(16)         0.7261        0.1009      0.3465
C(17)         0.6418        -0.0439     0.8543

N(1)          0.5324        0.0158      0.7182

O(1)          0.2257        0.1933      0.3470
O(2)          0.0560        0.2836      0.4306
O(3)          0.4616        0.0531      0.3097
O(4)          0.6481        0.1713      0.4393

H(1)          0.6210        0.1840      0.7230
H(2)          0.4640        0.2980      0.5170
H(3)          0.2820        0.2340      0.5830
H(4)          0.1930        0.0110      0.5730
H(5)          0.3050        -0.0240     0.4930
H(6)          0.3850        -0.0960     0.7770
H(7)          0.4090        0.0810      0.9760
H(8)          0.2870        0.1410      0.8610
H(9)          0.4440        0.3140      0.8150
H(10)         0.5560        0.2330      0.9400
H(11)         0.1580        0.1680      0.0530
H(12)         0.0640        0.2050      -0.2240
H(13)         -0.1470        0.3330      -0.3060
H(14)         -0.2320        0.4140      -0.103
H(15)         -0.1280        0.3810      0.186
H(16)         0.7330        0.0190      0.3810
H(17)         0.8130        0.1470      0.3710
H(18)         0.6990        0.1060      0.2370
H(19)         0.7250        -0.0340      0.836
H(20)         0.6470        -0.0070      0.961
H(21)         0.6230        -0.1410      0.861

Converting this to XYZ coordinates, namely to:

43
Cocaine 1983
C          0.5419        0.1631       0.7095
C          0.4579        0.2047       0.5345
C          0.3080        0.1713       0.5168
C          0.2903        0.0286       0.5727
C          0.3950        0.0004       0.7409
C          0.3870        0.1080       0.8678
C          0.4858        0.2192       0.8450
C          0.1028        0.2512       0.3219
C          0.0323        0.2713       0.1411
C          0.0857        0.2213       0.0238
C          0.0189        0.2435       -0.1419
C         -0.0995        0.3166        -0.1875
C         -0.1528        0.3671      -0.0719
C         -0.0880        0.3462      0.0951
C          0.5172        0.1331      0.4127
C          0.7261        0.1009      0.3465
C          0.6418        -0.0439     0.8543
N          0.5324        0.0158      0.7182
O          0.2257        0.1933      0.3470
O          0.0560        0.2836      0.4306
O          0.4616        0.0531      0.3097
O          0.6481        0.1713      0.4393
H          0.6210        0.1840      0.7230
H          0.4640        0.2980      0.5170
H          0.2820        0.2340      0.5830
H          0.1930        0.0110      0.5730
H          0.3050        -0.0240     0.4930
H          0.3850        -0.0960     0.7770
H          0.4090        0.0810      0.9760
H          0.2870        0.1410      0.8610
H          0.4440        0.3140      0.8150
H          0.5560        0.2330      0.9400
H          0.1580        0.1680      0.0530
H          0.0640        0.2050      -0.2240
H          -0.1470        0.3330      -0.3060
H          -0.2320        0.4140      -0.103
H          -0.1280        0.3810      0.186
H          0.7330        0.0190      0.3810
H          0.8130        0.1470      0.3710
H          0.6990        0.1060      0.2370
H          0.7250        -0.0340      0.836
H          0.6470        -0.0070      0.961
H          0.6230        -0.1410      0.861

Opening this with Accelrys gives this structure. https://i.stack.imgur.com/ijb19.png

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  • 1
    $\begingroup$ @AbelFriedman It is not cartesian coordinates. While xyz file is quite easy to construct, I can't guess an easy method to convert them, so it seems more convenient to find structure of compound of interest in more suitable form. $\endgroup$
    – permeakra
    Oct 18, 2014 at 17:05
  • $\begingroup$ @permeakra: Wikipedia has the transformation matrix for fractional coordinates to cartesian coordinates. The crystal system is monoclinic, which makes the transformation rather painless, nothing that a few lines of awk won't do. $\endgroup$
    – Abel Friedman
    Oct 18, 2014 at 19:45
  • $\begingroup$ Although its now old rasmol and rasmac is very relaxed about exact format as long as the atom type appear after the coordinates. Its also free, and very fast to use if you need to rotate large protein models. It will do most simple angle and distance calculations etc. Basic, but very useful for quick look stuff. $\endgroup$
    – porphyrin
    Jul 20, 2016 at 12:06

1 Answer 1

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Generally speaking, babel from the Openbabel suite will convert chemical file formats. The openbabel wiki has a page with examples on input in free-form fractional coordinate format, and the abstract of the paper has the unit cell dimensions.

Single CIF files can be requested from the Cambridge Crystallographic Data Centre.

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    $\begingroup$ +1 Indeed, this would be my exact answer. It's the reason I added "free form fractional" to babel, since you run across this problem in older papers. $\endgroup$
    – Geoff Hutchison
    Oct 18, 2014 at 20:36
  • $\begingroup$ I have a first year chem knowledge, so at the moment I haven't the foggiest as to what "free-form fractional coordinate format" means. I made that request but they don't have such a CIF file at this data centre. $\endgroup$
    – Josh Pinto
    Oct 18, 2014 at 21:31
  • 1
    $\begingroup$ @BrentonHorne: It's an oblique coordinate system formed by the unit cell of the crystal. The angles between the axes are the angles of the unit cell, and the units are dimensionless and expressed in terms of the edges of the unit cell. $\endgroup$
    – Abel Friedman
    Oct 18, 2014 at 22:23
  • $\begingroup$ OK, how do I do that for my example? I have no idea what to set the unit cell as. $\endgroup$
    – Josh Pinto
    Oct 18, 2014 at 22:47
  • $\begingroup$ @BrentonHorne: Look no further than the abstract for unit cell parameters: a, b, c, \beta. \alpha == \gamma == 90 deg, since the crystal system is monoclinic. $\endgroup$
    – Abel Friedman
    Oct 19, 2014 at 0:10

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