From owner-chemistry@ccl.net Sun Jan  8 15:04:00 2012
From: "Andrew DeYoung andrewdaviddeyoung- -gmail.com" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: What is the format of this file containing Cartesian coordinates?
Message-Id: <-46122-120108145009-21030-npaEEgkIzIjXbLvJfIMzTQ*server.ccl.net>
X-Original-From: Andrew DeYoung <andrewdaviddeyoung++gmail.com>
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Date: Sun, 8 Jan 2012 14:50:02 -0500
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Sent to CCL by: Andrew DeYoung [andrewdaviddeyoung*|*gmail.com]
Hi,

I have been reading the paper "Modeling of Graphite Oxide,"
Boukhvalov, D. W.; Katsnelson, M. I., J. Am. Chem. Soc. 2008, 130,
10697-10701.  This paper has Supporting Information associated with
it, located here: http://pubs.acs.org/doi/suppl/10.1021/ja8021686 .
This Supporting Information contains the Cartesian coordinates for
various chemical species discussed in the paper (obtained by ab initio
calculations).  For example, one of the series of coordinates that
this Supporting Information provides is the following:

-0.02689401 0.05432733 1.07516282 3 H 1
0.03282702 -0.01179385 0.68330051 2 O 2
0.60586594 -0.05478650 -1.06215854 3 H 3
0.54625340 0.01126245 -0.67028541 2 O 4
-0.00037430 0.00545262 0.11451905 1 C 5
-0.87007097 0.50375034 -0.04749619 1 C 6
-0.86607388 -0.50142967 -0.04692549 1 C 7
0.87536552 0.51049597 0.02025204 1 C 8
0.87795979 -0.51877321 0.02366501 1 C 9
-0.00283324 1.00386837 -0.01257709 1 C 10
0.00039748 -1.00136092 -0.01066833 1 C 11
-1.73307292 0.00197123 -0.03871588 1 C 12
-0.86683173 1.50543512 -0.02856670 1 C 13
-0.86909689 -1.50476823 -0.02691608 1 C 14
1.73809709 0.00167020 0.06437659 1 C 15
0.86891453 1.50286912 0.03907748 1 C 16
0.87181125 -1.50614862 0.04060303 1 C 17
-1.73625671 1.00707540 -0.04218536 1 C 18
-1.73743458 -1.00321958 -0.04099753 1 C 19
1.73948240 1.00519036 0.06254294 1 C 20
1.73748379 -1.00684011 0.06397068 1 C 21
-0.00097315 2.00519687 -0.00474136 1 C 22
-0.00025493 -2.00481803 -0.00256281 1 C 23
-2.60679486 0.50744858 -0.05730558 1 C 24
-2.60244033 -0.49997860 -0.05660149 1 C 25
-1.73600183 2.00826255 -0.03828653 1 C 26
-1.73589004 -2.00632024 -0.03581581 1 C 27
-0.86809971 2.50743539 -0.01969374 1 C 28
-0.86743107 -2.50800945 -0.01663035 1 C 29
1.73739025 -2.00803386 0.03602309 1 C 30
0.86918912 -2.50605556 0.01898868 1 C 31
-2.60674237 1.50998962 -0.06149746 1 C 32
-2.60337977 -1.50359739 -0.05952099 1 C 33
-0.00151756 3.01254125 0.00026303 1 C 34
-1.73833995 3.01353076 -0.04134158 1 C 35
1.73896850 -3.01089377 0.04144619 1 C 36
-2.60747482 2.51319434 -0.06379837 1 C 37
0.87160242 -3.51651549 0.01963025 1 C 38
-2.60959081 3.52137327 -0.06444686 1 C 39
1.74167046 -4.01903762 0.03732286 1 C 40
0.57935253 -0.00591929 -0.10150666 1 C 41
-0.29895259 0.51824224 -0.01065610 1 C 42
-0.29637000 -0.51095564 -0.00724144 1 C 43
-1.15911004 -0.00215128 -0.05137018 1 C 44
0.57861451 1.00085598 0.02367761 1 C 45
0.58190077 -1.00453933 0.02559150 1 C 46
-1.15848220 1.00634128 -0.05096692 1 C 47
-1.16048708 -1.00566650 -0.04953595 1 C 48
1.44505788 0.50095217 0.05994684 1 C 49
1.44905447 -0.50423433 0.06052232 1 C 50
-0.29287191 1.50575663 -0.02758935 1 C 51
-0.28990959 -1.50337425 -0.02606221 1 C 52
-2.02697593 0.50391544 -0.04217217 1 C 53
-2.02491349 -0.50419505 -0.04152028 1 C 54
1.44809109 1.50425324 0.03991273 1 C 55
1.44587383 -1.50598582 0.04156281 1 C 56
0.57921418 2.00435850 0.01557045 1 C 57
0.58001551 -2.00575731 0.01775155 1 C 58
-1.15838843 2.00756158 -0.02302302 1 C 59
-1.15757535 -2.00795444 -0.02057379 1 C 60
2.31207394 -0.00245438 0.05172946 1 C 61
-2.02776434 1.50719055 -0.04446594 1 C 62
-2.02602610 -1.50572182 -0.04269775 1 C 63
2.31642963 1.00271453 0.05400912 1 C 64
2.31524228 -1.00755964 0.05519446 1 C 65
-0.29021505 2.50557497 -0.00598370 1 C 66
-0.28747789 -2.51054533 -0.00287556 1 C 67
1.44708230 -2.50791413 0.03270193 1 C 68
2.31499473 -2.00876451 0.05130262 1 C 69
0.58051995 -3.01303700 0.01275161 1 C 70
-2.02771967 2.50972812 -0.04865231 1 C 71
-1.15998355 3.01040245 -0.02842868 1 C 72
2.31732484 -3.01400623 0.05435683 1 C 73
1.45151430 -3.51897104 0.03339008 1 C 74
-2.03208004 3.51717648 -0.04935652 1 C 75
2.31999134 -4.02068999 0.05257440 1 C 76

However, the Supporting Information (nor the article itself) appears
to specify the type of coordinate file that they are providing.  For
example, is this in PDB format, XYZ format, or another format?  Can
anyone please help me know which format this might be so that I can
save it in an appropriate file type and visualize the structure using
VMD?

Thank you kindly!

Andrew DeYoung
Carnegie Mellon University


From owner-chemistry@ccl.net Sun Jan  8 17:14:00 2012
From: "Edward Holland hollandej~~Cardiff.ac.uk" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL: What is the format of this file containing Cartesian coordinates?
Message-Id: <-46123-120108171055-5964-eRIrALpTpcdIpFD5PcJirg _ server.ccl.net>
X-Original-From: Edward Holland <hollandej^_^Cardiff.ac.uk>
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Date: Sun, 8 Jan 2012 22:10:41 +0000
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Sent to CCL by: Edward Holland [hollandej!^!Cardiff.ac.uk]

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Hi,
Handy tip: You can copy and paste many common formats directly into =
Avogadro (Main Page - Avogadro - Free cross-platform molecule editor) =
You can then visualise it here or save into a format you are more =
familiar with.

Yours

Ed Holland
=20
On 8 Jan 2012, at 19:50, Andrew DeYoung andrewdaviddeyoung- -gmail.com =
wrote:

> -0.02689401 0.05432733 1.07516282 3 H 1
> 0.03282702 -0.01179385 0.68330051 2 O 2
> 0.60586594 -0.05478650 -1.06215854 3 H 3
> 0.54625340 0.01126245 -0.67028541 2 O 4
> -0.00037430 0.00545262 0.11451905 1 C 5
> -0.87007097 0.50375034 -0.04749619 1 C 6
> -0.86607388 -0.50142967 -0.04692549 1 C 7
> 0.87536552 0.51049597 0.02025204 1 C 8
> 0.87795979 -0.51877321 0.02366501 1 C 9
> -0.00283324 1.00386837 -0.01257709 1 C 10
> 0.00039748 -1.00136092 -0.01066833 1 C 11
> -1.73307292 0.00197123 -0.03871588 1 C 12
> -0.86683173 1.50543512 -0.02856670 1 C 13
> -0.86909689 -1.50476823 -0.02691608 1 C 14
> 1.73809709 0.00167020 0.06437659 1 C 15
> 0.86891453 1.50286912 0.03907748 1 C 16
> 0.87181125 -1.50614862 0.04060303 1 C 17
> -1.73625671 1.00707540 -0.04218536 1 C 18
> -1.73743458 -1.00321958 -0.04099753 1 C 19
> 1.73948240 1.00519036 0.06254294 1 C 20
> 1.73748379 -1.00684011 0.06397068 1 C 21
> -0.00097315 2.00519687 -0.00474136 1 C 22
> -0.00025493 -2.00481803 -0.00256281 1 C 23
> -2.60679486 0.50744858 -0.05730558 1 C 24
> -2.60244033 -0.49997860 -0.05660149 1 C 25
> -1.73600183 2.00826255 -0.03828653 1 C 26
> -1.73589004 -2.00632024 -0.03581581 1 C 27
> -0.86809971 2.50743539 -0.01969374 1 C 28
> -0.86743107 -2.50800945 -0.01663035 1 C 29
> 1.73739025 -2.00803386 0.03602309 1 C 30
> 0.86918912 -2.50605556 0.01898868 1 C 31
> -2.60674237 1.50998962 -0.06149746 1 C 32
> -2.60337977 -1.50359739 -0.05952099 1 C 33
> -0.00151756 3.01254125 0.00026303 1 C 34
> -1.73833995 3.01353076 -0.04134158 1 C 35
> 1.73896850 -3.01089377 0.04144619 1 C 36
> -2.60747482 2.51319434 -0.06379837 1 C 37
> 0.87160242 -3.51651549 0.01963025 1 C 38
> -2.60959081 3.52137327 -0.06444686 1 C 39
> 1.74167046 -4.01903762 0.03732286 1 C 40
> 0.57935253 -0.00591929 -0.10150666 1 C 41
> -0.29895259 0.51824224 -0.01065610 1 C 42
> -0.29637000 -0.51095564 -0.00724144 1 C 43
> -1.15911004 -0.00215128 -0.05137018 1 C 44
> 0.57861451 1.00085598 0.02367761 1 C 45
> 0.58190077 -1.00453933 0.02559150 1 C 46
> -1.15848220 1.00634128 -0.05096692 1 C 47
> -1.16048708 -1.00566650 -0.04953595 1 C 48
> 1.44505788 0.50095217 0.05994684 1 C 49
> 1.44905447 -0.50423433 0.06052232 1 C 50
> -0.29287191 1.50575663 -0.02758935 1 C 51
> -0.28990959 -1.50337425 -0.02606221 1 C 52
> -2.02697593 0.50391544 -0.04217217 1 C 53
> -2.02491349 -0.50419505 -0.04152028 1 C 54
> 1.44809109 1.50425324 0.03991273 1 C 55
> 1.44587383 -1.50598582 0.04156281 1 C 56
> 0.57921418 2.00435850 0.01557045 1 C 57
> 0.58001551 -2.00575731 0.01775155 1 C 58
> -1.15838843 2.00756158 -0.02302302 1 C 59
> -1.15757535 -2.00795444 -0.02057379 1 C 60
> 2.31207394 -0.00245438 0.05172946 1 C 61
> -2.02776434 1.50719055 -0.04446594 1 C 62
> -2.02602610 -1.50572182 -0.04269775 1 C 63
> 2.31642963 1.00271453 0.05400912 1 C 64
> 2.31524228 -1.00755964 0.05519446 1 C 65
> -0.29021505 2.50557497 -0.00598370 1 C 66
> -0.28747789 -2.51054533 -0.00287556 1 C 67
> 1.44708230 -2.50791413 0.03270193 1 C 68
> 2.31499473 -2.00876451 0.05130262 1 C 69
> 0.58051995 -3.01303700 0.01275161 1 C 70
> -2.02771967 2.50972812 -0.04865231 1 C 71
> -1.15998355 3.01040245 -0.02842868 1 C 72
> 2.31732484 -3.01400623 0.05435683 1 C 73
> 1.45151430 -3.51897104 0.03339008 1 C 74
> -2.03208004 3.51717648 -0.04935652 1 C 75
> 2.31999134 -4.02068999 0.05257440 1 C 76


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<html><head></head><body style=3D"word-wrap: break-word; =
-webkit-nbsp-mode: space; -webkit-line-break: after-white-space; =
">Hi,<div>Handy tip: You can copy and paste many common formats directly =
into Avogadro (<a =
href=3D"http://www.google.co.uk/url?sa=3Dt&amp;rct=3Dj&amp;q=3Davogadro&am=
p;source=3Dweb&amp;cd=3D3&amp;ved=3D0CEIQFjAC&amp;url=3Dhttp://avogadro.op=
enmolecules.net/&amp;ei=3DCBQKT5iTMsG48gPHhqThBA&amp;usg=3DAFQjCNHr_SlSBj4=
WlbLK43ocrL9gyz856Q">Main Page - Avogadro - Free cross-platform molecule =
editor</a>) You can then visualise it here or save into a format you are =
more familiar =
with.</div><div><br></div><div>Yours</div><div><br></div><div>Ed =
Holland</div><div>&nbsp;</div><div><div><div>On 8 Jan 2012, at 19:50, =
Andrew DeYoung andrewdaviddeyoung- <a =
href=3D"http://-gmail.com">-gmail.com</a> wrote:</div><br =
class=3D"Apple-interchange-newline"><blockquote type=3D"cite">-0.02689401 =
0.05432733 1.07516282 3 H 1<br>0.03282702 -0.01179385 0.68330051 2 O =
2<br>0.60586594 -0.05478650 -1.06215854 3 H 3<br>0.54625340 0.01126245 =
-0.67028541 2 O 4<br>-0.00037430 0.00545262 0.11451905 1 C =
5<br>-0.87007097 0.50375034 -0.04749619 1 C 6<br>-0.86607388 -0.50142967 =
-0.04692549 1 C 7<br>0.87536552 0.51049597 0.02025204 1 C =
8<br>0.87795979 -0.51877321 0.02366501 1 C 9<br>-0.00283324 1.00386837 =
-0.01257709 1 C 10<br>0.00039748 -1.00136092 -0.01066833 1 C =
11<br>-1.73307292 0.00197123 -0.03871588 1 C 12<br>-0.86683173 =
1.50543512 -0.02856670 1 C 13<br>-0.86909689 -1.50476823 -0.02691608 1 C =
14<br>1.73809709 0.00167020 0.06437659 1 C 15<br>0.86891453 1.50286912 =
0.03907748 1 C 16<br>0.87181125 -1.50614862 0.04060303 1 C =
17<br>-1.73625671 1.00707540 -0.04218536 1 C 18<br>-1.73743458 =
-1.00321958 -0.04099753 1 C 19<br>1.73948240 1.00519036 0.06254294 1 C =
20<br>1.73748379 -1.00684011 0.06397068 1 C 21<br>-0.00097315 2.00519687 =
-0.00474136 1 C 22<br>-0.00025493 -2.00481803 -0.00256281 1 C =
23<br>-2.60679486 0.50744858 -0.05730558 1 C 24<br>-2.60244033 =
-0.49997860 -0.05660149 1 C 25<br>-1.73600183 2.00826255 -0.03828653 1 C =
26<br>-1.73589004 -2.00632024 -0.03581581 1 C 27<br>-0.86809971 =
2.50743539 -0.01969374 1 C 28<br>-0.86743107 -2.50800945 -0.01663035 1 C =
29<br>1.73739025 -2.00803386 0.03602309 1 C 30<br>0.86918912 -2.50605556 =
0.01898868 1 C 31<br>-2.60674237 1.50998962 -0.06149746 1 C =
32<br>-2.60337977 -1.50359739 -0.05952099 1 C 33<br>-0.00151756 =
3.01254125 0.00026303 1 C 34<br>-1.73833995 3.01353076 -0.04134158 1 C =
35<br>1.73896850 -3.01089377 0.04144619 1 C 36<br>-2.60747482 2.51319434 =
-0.06379837 1 C 37<br>0.87160242 -3.51651549 0.01963025 1 C =
38<br>-2.60959081 3.52137327 -0.06444686 1 C 39<br>1.74167046 =
-4.01903762 0.03732286 1 C 40<br>0.57935253 -0.00591929 -0.10150666 1 C =
41<br>-0.29895259 0.51824224 -0.01065610 1 C 42<br>-0.29637000 =
-0.51095564 -0.00724144 1 C 43<br>-1.15911004 -0.00215128 -0.05137018 1 =
C 44<br>0.57861451 1.00085598 0.02367761 1 C 45<br>0.58190077 =
-1.00453933 0.02559150 1 C 46<br>-1.15848220 1.00634128 -0.05096692 1 C =
47<br>-1.16048708 -1.00566650 -0.04953595 1 C 48<br>1.44505788 =
0.50095217 0.05994684 1 C 49<br>1.44905447 -0.50423433 0.06052232 1 C =
50<br>-0.29287191 1.50575663 -0.02758935 1 C 51<br>-0.28990959 =
-1.50337425 -0.02606221 1 C 52<br>-2.02697593 0.50391544 -0.04217217 1 C =
53<br>-2.02491349 -0.50419505 -0.04152028 1 C 54<br>1.44809109 =
1.50425324 0.03991273 1 C 55<br>1.44587383 -1.50598582 0.04156281 1 C =
56<br>0.57921418 2.00435850 0.01557045 1 C 57<br>0.58001551 -2.00575731 =
0.01775155 1 C 58<br>-1.15838843 2.00756158 -0.02302302 1 C =
59<br>-1.15757535 -2.00795444 -0.02057379 1 C 60<br>2.31207394 =
-0.00245438 0.05172946 1 C 61<br>-2.02776434 1.50719055 -0.04446594 1 C =
62<br>-2.02602610 -1.50572182 -0.04269775 1 C 63<br>2.31642963 =
1.00271453 0.05400912 1 C 64<br>2.31524228 -1.00755964 0.05519446 1 C =
65<br>-0.29021505 2.50557497 -0.00598370 1 C 66<br>-0.28747789 =
-2.51054533 -0.00287556 1 C 67<br>1.44708230 -2.50791413 0.03270193 1 C =
68<br>2.31499473 -2.00876451 0.05130262 1 C 69<br>0.58051995 -3.01303700 =
0.01275161 1 C 70<br>-2.02771967 2.50972812 -0.04865231 1 C =
71<br>-1.15998355 3.01040245 -0.02842868 1 C 72<br>2.31732484 =
-3.01400623 0.05435683 1 C 73<br>1.45151430 -3.51897104 0.03339008 1 C =
74<br>-2.03208004 3.51717648 -0.04935652 1 C 75<br>2.31999134 =
-4.02068999 0.05257440 1 C 76</blockquote></div><br></div></body></html>=

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