Hello,

=

I need to plot about 50 mopac input structures with titles on a page(= s) given a list of file names.=C2=A0 I would appreciate any suggestions. Ex= cept for hetero atoms, hydrogen could be omitted.

Many thanks!=

John

John McKelvey
545 Lega= cy Pointe Dr

O'Fallon, MO 63376
636-294-5203
jmmckel[a]gmail.com

--001a113f8f6092fbd7052911e730-- From owner-chemistry@ccl.net Tue Jan 12 09:12:01 2016 From: "Michel Petitjean petitjean.chiral__gmail.com" To: CCL Subject: CCL: Plotting multiple file structures Message-Id: <-51959-160112090607-12892-FJ9prKwRvRS13vAbZu8+Xw=-=server.ccl.net> X-Original-From: Michel Petitjean Content-Type: multipart/alternative; boundary=001a11c37c54b539c70529238da6 Date: Tue, 12 Jan 2016 15:06:01 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral###gmail.com] --001a11c37c54b539c70529238da6 Content-Type: text/plain; charset=UTF-8 If you are a latex user, save your structures in image files then use the tabular or longtable environment with appropriate includegraphics commands. If you are a Word user, sorry, I cannot help. Best regards, Michel. Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral{:}gmail.com (preferred), michel.petitjean{:}univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html 2016-01-11 18:02 GMT+01:00 John McKelvey jmmckel a gmail.com < owner-chemistry{:}ccl.net>: > > Hello, > > I need to plot about 50 mopac input structures with titles on a page(s) > given a list of file names. I would appreciate any suggestions. Except for > hetero atoms, hydrogen could be omitted. > > Many thanks! > > John > -- > John McKelvey > 545 Legacy Pointe Dr > O'Fallon, MO 63376 > 636-294-5203 > jmmckel\a/gmail.com > --001a11c37c54b539c70529238da6 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

If you are a latex user, save your structures in= image files then use the tabular or longtable environment with appropriate= includegraphics commands.

If you are a Word user, sorry, I cannot= help.
Best regards,

Michel.

Michel Petitjean
MTi, IN= SERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Ced= ex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: petitjean.chiral{:}gmail.com (= preferred),
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 michel.petitjean{:}univ-paris-didero= t.fr
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html

2016-01-11 1= 8:02 GMT+01:00 John McKelvey jmmckel a gmail.c= om <owner-chemistry{:}ccl.net>:

= Hello,

I need to plot about 50 mopac input structures with tit= les on a page(s) given a list of file names.=C2=A0 I would appreciate any s= uggestions. Except for hetero atoms, hydrogen could be omitted.

Many thanks!

John
=
--
John= McKelvey
545 Legacy Pointe Dr
O'Fallon, MO 63376
636-294-52= 03
jmmcke= l\a/gmail.com

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Hutchison [geoffh^_^pitt.edu] --Apple-Mail=_3ECFF1BC-BA69-49F9-B882-901B75465139 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Actually if you're using Open Babel, you want to use the SVG format, = which can then be converted to PDF or whatever by a graphics program. = There are a bunch of options to control the formatting of the output: = http://baoilleach.blogspot.com/2011/06/molecular-zooming-with-open-babel-s= vg.html = http://open-babel.readthedocs.org/en/latest/FileFormats/SVG_2D_depiction.h= tml#svg-2d-depiction # convert all MOPAC output files to an SVG grid after condensing aliases obabel *.out O out.svg --genalias -xA Of course my question would be whether you want Mopac *input* or = *output* There are also a few options to output a pseudo-3D format in the current = development code (e.g., it's a 2D diagram, but it looks like = balls-and-sticks). --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh(a)pitt.edu web: http://hutchison.chem.pitt.edu/ > I am assuming you want 2D structures. If so I would use Openbabel to = convert to SDF or CDX format. Assuming you have Chemdraw you could read = them in, organize on the pages and print. Not the best solution, but it = should work. Bill ... > I need to plot about 50 mopac input structures with titles on a = page(s) given a list of file names. I would appreciate any suggestions. = Except for hetero atoms, hydrogen could be omitted >=20 --Apple-Mail=_3ECFF1BC-BA69-49F9-B882-901B75465139 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii

Actually if you're using Open Babel, you want to use the = SVG format, which can then be converted to PDF or whatever by a graphics = program. There are a bunch of options to control the formatting of the = output:

http://baoilleach.blogspot.com/2011/06/molecular-zooming-with-o= pen-babel-svg.html

http://open-babel.readthedocs.org/en/latest/FileFormats/SVG_2D_= depiction.html#svg-2d-depiction

# = convert all MOPAC output files to an SVG grid after condensing = aliases

obabel *.out O out.svg --genalias -xA

Of course my question would be whether you want = Mopac *input* or *output*

There are = also a few options to output a pseudo-3D format in the current = development code (e.g., it's a 2D diagram, but it looks like = balls-and-sticks).

---

Prof. Geoffrey = Hutchison

Department of Chemistry

University of = Pittsburgh

tel: (412) 648-0492

email: geoffh(a)pitt.edu

web: http://hutchison.chem.pitt.edu/

I = am assuming you want 2D structures. If so I would use Openbabel to = convert to SDF or CDX format. Assuming you have Chemdraw you could = read them in, organize on the pages and print. Not the best = solution, but it should work. Bill

...

I need to plot about 50 mopac input structures with = titles on a page(s) given a list of file names. I would appreciate = any suggestions. Except for hetero atoms, hydrogen could be omitted