From owner-chemistry@ccl.net Wed Feb 15 05:33:00 2012 From: "Lu s Pinto da Silva luist311\a/hotmail.com" To: CCL Subject: CCL:G: Error in the calculations Message-Id: <-46291-120215053213-4748-7eLbUZAueechymmo1cTGpA-,-server.ccl.net> X-Original-From: "Lu s Pinto da Silva" Date: Wed, 15 Feb 2012 05:32:11 -0500 Sent to CCL by: "Lu s Pinto da Silva" [luist311.:.hotmail.com] Hi, I am performing single point energy calculations (with G03) in a molecule both in vacuo and surronded by water molecules. However, the first calculation terminates with the error "**** Fatal Problem: The smallest alpha delta epsilon is 0.95715345D-03", while the second finishes without problem. What may be the problem with the first calculation, which doesn't affect the second calculation? Best Regards. From owner-chemistry@ccl.net Wed Feb 15 07:34:00 2012 From: "eurisco1%x%pochta.ru" To: CCL Subject: CCL:G: computational error Message-Id: <-46292-120215072310-5877-zAf661SsH3X55gS09N0HhQ-*-server.ccl.net> X-Original-From: Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="koi8-r"; reply-type=original Date: Wed, 15 Feb 2012 16:22:35 +0400 MIME-Version: 1.0 Sent to CCL by: [eurisco1()pochta.ru] Dear kiran kumar nalla, The keyword opt(cartesian) will treat the problem. Sincerely, Ol Ga -----éÓÈÏÄÎÏÅ ÓÏÏÂÝÅÎÉÅ----- > From: kiran kumar nalla kiran.nalla1984]~[gmail.com Sent: Wednesday, February 15, 2012 3:30 AM To: Ga, Ol Subject: CCL:G: computational error Sent to CCL by: "kiran kumar nalla" [kiran.nalla1984- -gmail.com] hi i am trying to optimize peptide with transition metal ions and find the potential binding site on the peptide using gaussian but i got error stating Error in internal coordinate system. Error termination via Lnk1e in /var/gaussian/g09/l103.exe at Tue Feb 14 16:35:10 2012. Job cpu time: 0 days 0 hours 1 minutes 20.2 seconds. File lengths (MBytes): RWF= 667 Int= 0 D2E= 0 Chk= 16 i need help to reset this problem. i am very poor in computational chemistry but all my work is related to that if any one can help me fix this and some useful links to learn comutational plzz i need help very urgently kiran kumar nalla kiran.nalla1984_._gmail.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Feb 15 08:11:00 2012 From: "Saman Mandegar mandegar_saman(~)yahoo.com" To: CCL Subject: CCL: differenence between energy gap in DFT and HF Message-Id: <-46293-120215080842-12709-+OoiMN6fSgbzGqkl1RuueA!=!server.ccl.net> X-Original-From: "Saman Mandegar" Date: Wed, 15 Feb 2012 08:08:41 -0500 Sent to CCL by: "Saman Mandegar" [mandegar_saman++yahoo.com] Dear All, I am sorry for multiple sending. I would like to generate the orbitals for using in a CASSCF calculation. I I have read following statement. but I am not pretty sure I understand it fully. and what is the difference between KS orbitals an HF and which one is better to use as initial orbitals for CASSCF calculations? "The orbital energy differences in Kohn Sham are more nearly like excitation energies which the equivalent quantities in Hartree Fock correspond to the electron detachment/attachment. This is why DFT is almost invariably better that Hartree Fock for generating the orbital for using in the active space in CASSCF." I would be very happy if any body could explain this in details. Many thanks for your comments in advance. Saman From owner-chemistry@ccl.net Wed Feb 15 09:17:00 2012 From: "uekstrom . gmail.com uekstrom . gmail.com" To: CCL Subject: CCL: differenence between energy gap in DFT and HF Message-Id: <-46294-120215091557-32495-UGHowgqKglTiwrZ6nR4SDg===server.ccl.net> X-Original-From: "uekstrom]*[gmail.com" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 15 Feb 2012 15:15:50 +0100 MIME-Version: 1.0 Sent to CCL by: "uekstrom+/-gmail.com" [uekstrom+/-gmail.com] > "The orbital energy differences in Kohn Sham are more nearly like excitation energies which the equivalent quantities in Hartree Fock correspond to the electron detachment/attachment. This is why DFT is almost invariably better that Hartree Fock for generating the orbital for using in the active space in CASSCF." The reason that the DFT orbitals are better is that the virtual DFT orbitals "see" a charged N-1 electron system, while the HF virtual orbitals "see" a neutral system. This makes the HF orbitals too diffuse for the CAS. You can improve the virtual HF orbitals with a simple point charge model, see C. W. Bauschlicher, Jr., The construction of modified virtual orbitals (MVO's) which are suited for configuration interaction calculations, J. Chem. Phys. 72, 880 (1980). For pure functionals that are constructed for correct excitation energies (LB94, SAOP etc) the virtuals look a lot like the MVO's. It is interesting to see that if you use hybrid functionals the virtuals look more and more like the HF orbitals when you increase the amount of HF exchange. At the same time orbital mixing "during the excitation" becomes more important. You can also see that LDA virtuals are nowhere near the "correct" shape, but they are still much more compact than HF orbitals and may be fine for use in a CASSF. So I would say that it's the orbital shape that is important, not the energy. In any case the DFT orbital energies do not enter into a CASSCF calculation except possibly through the selection of the active space. Sincerely, Ulf Ekstrom, Oslo University. From owner-chemistry@ccl.net Wed Feb 15 10:34:01 2012 From: "Flick Coleman wcoleman[A]wellesley.edu" To: CCL Subject: CCL: Good Vibrations Message-Id: <-46295-120214092057-25474-macwAnJ9JPFxUYtEEXHzVw_._server.ccl.net> X-Original-From: Flick Coleman Content-Type: multipart/alternative; boundary=e89a8f22beefdd82c904b8ed4cf3 Date: Tue, 14 Feb 2012 09:20:03 -0500 MIME-Version: 1.0 Sent to CCL by: Flick Coleman [wcoleman]-[wellesley.edu] --e89a8f22beefdd82c904b8ed4cf3 Content-Type: text/plain; charset=ISO-8859-1 For a number of years I have introduced vibrational calculations and vibrational motion using a web page I created with the song as background. Cheers, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 www.wellesley.edu/Chemistry/colemanw.html www.flicksstuff.com/photos/pictures.html new galleries coming soon On Tue, Feb 14, 2012 at 7:50 AM, Roger Robinson scu98rkr+/-gmail.com < owner-chemistry*ccl.net> wrote: > Hi All, > > While working today "Good Vibrations" by the Beach boys came on in the > background on Last.fm. > > Has it ever occured to anyone that Good Vibrations might be about the > formation of Excited states and the vibrational frequencies seen in > emission spectra of molecules ? > > Explanation below. > > Roger > > > > Ah! I love the colorful clothes she wears (*she's the atom and he's > interested in the vibration frequencies (colours) produced by emission*) > And the way the sunlight plays upon her hair (*UV light shone upon atom.* > *Strands of hair describe different energy levels*) > Ah! I hear the sound of a gentle word (*Absorbtion of UV light*) > On the wind that lifts her perfume through the air (*electron moved up to > higher energy level*) > > Refrain: > > I'm pickin' up good vibrations (*He's a scientist emission spectroscopy* ) > She's givin' me the excitations (*she is the atom*) > I'm pickin' up good vibrations > (Ooo, bop-bop, good vibrations) > She's givin' me the excitations > (Bop-bop, excitations) > (Good, good, good, good vibrations) > I'm pickin' up good vibrations > (Ooo, bop-bop, good vibrations) > She's givin' me the excitation > (Bop-bop, excitations) > (Good, good, good, good vibrations) > I'm pickin' up good vibrations > (Ooo, bop-bop, good vibrations) > She's givin' me the excitations > (Bop-bop, excitations) > > Close my eyes; she's somehow closer now (*He's finsihed the analysis and > understands the material better*) > Softly smile I know she must be kind (*same sort of thing*) > When -- I look in her eyes > She goes with me to a blossom world > > {Refrain} > > I don't know where, but she sends me there > (Oh, my my love sensation) > (Oh, my my heart elation) > > Gotta keep those lovin' good vibrations a-happenin' with her x3 > > Ohh! > > (Good, good, good, good vibrations) > I'm pickin' up good vibrations > (Ooo, bop-bop, good vibrations) > She's givin' me the excitation > (Bop-bop, excitations) > (Good, good, good, good vibrations) > I'm pickin' up good vibrations > (Ooo, bop-bop, good vibrations) > --e89a8f22beefdd82c904b8ed4cf3 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable For a number of y= ears I have introduced vibrational calculations and vibrational motion usin= g a web page I created with the song as background.


Cheers,

Flick

_______________
William F. Coleman
Profess= or of Chemistry
Wellesley College
Wellesl= ey MA 02481

= www= .wellesley.edu/Chemistry/colemanw.html
www.= flicksstuff.com/photos/pictures.html new galleries coming soon




On Tue, Feb 14, 2012 at 7:50 AM, Roger R= obinson scu98rkr+/-gmail.com <owner-chemistry*ccl.net= > wrote:
=20 =20 =20
Hi All,

While working today "Good Vibrations" by the Beach boys came = on in the background on Last.fm.

Has it ever occured to anyone that Good Vibrations might be about the formation of Excited states and the vibrational frequencies seen in emission spectra of molecules ?

Explanation below.

Roger



Ah! I love the colorful clothes she wears (she's the atom and he's interested in the vibration frequencies (colours) produced b= y emission)
And the way the sunlight plays upon her hair (UV light shone upon atom. Strands of hair describe different energy levels) Ah! I hear the sound of a gentle word (Absorbtion of UV light) On the wind that lifts her perfume through the air (electron moved up to higher energy level)

Refrain:

I'm pickin' up good vibrations (He's a scientist emissio= n spectroscopy )
She's givin' me the excitations (she is the atom)
I'm pickin' up good vibrations
(Ooo, bop-bop, good vibrations)
She's givin' me the excitations
(Bop-bop, excitations)
(Good, good, good, good vibrations)
I'm pickin' up good vibrations
(Ooo, bop-bop, good vibrations)
She's givin' me the excitation
(Bop-bop, excitations)
(Good, good, good, good vibrations)
I'm pickin' up good vibrations
(Ooo, bop-bop, good vibrations)
She's givin' me the excitations
(Bop-bop, excitations)

Close my eyes; she's somehow closer now (He's finsihed the analysis and understands the material better)
Softly smile I know she must be kind (same sort of thing)
When -- I look in her eyes
She goes with me to a blossom world

{Refrain}

I don't know where, but she sends me there
(Oh, my my love sensation)
(Oh, my my heart elation)

Gotta keep those lovin' good vibrations a-happenin' with her x3=

Ohh!

(Good, good, good, good vibrations)
I'm pickin' up good vibrations
(Ooo, bop-bop, good vibrations)
She's givin' me the excitation
(Bop-bop, excitations)
(Good, good, good, good vibrations)
I'm pickin' up good vibrations
(Ooo, bop-bop, good vibrations)

--e89a8f22beefdd82c904b8ed4cf3-- From owner-chemistry@ccl.net Wed Feb 15 11:09:01 2012 From: "Daniel Cappel daniel.cappel() schrodinger.com" To: CCL Subject: CCL: Creating "cartoony" molecular images Message-Id: <-46296-120215030231-5190-MgYm9BVfelGV4bJrYj6S0g[A]server.ccl.net> X-Original-From: Daniel Cappel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 15 Feb 2012 09:02:00 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Cappel [daniel.cappel!^!schrodinger.com] Hi Billy! You should have a look at PyMOL, a user-sponsored open-source visualization tool. www.pymol.org Therewith you can set different, so called, ray_trace_modes. This allows you to create images with a cartoony appearance. For a few examples have a look at this wiki page. http://www.pymolwiki.org/index.php/Ray#Modes Of course this also works for small molecules and not only for proteins as shown in these examples. Best, Daniel On Wed, Feb 15, 2012 at 12:58 AM, Billy McCann bwm0005() tigermail.auburn.edu wrote: > > Sent to CCL by: Billy McCann [bwm0005 * tigermail.auburn.edu] > Greetings All. > > I'm attempting to create molecular images which are very "cartoony" in nature, i.e. no lighting or shine on the atoms, bonds represented as thick black lines, etc. > > For example, see the following image linked below: > http://www.auburn.edu/~bwm0005/sample2.jpg > > The software which was previously used is designed for an outdated platform (classic Mac) and so I'm searching for a replacement.  I've tried many of the popular molecular imaging programs, but most create plastic and/or metallic looking images even after tweaking the settings. > > The product with which I've come closest is Chemcraft.  I adjusted the configuration of the trial-ware version to produce the following image, which is very close to my goal: > http://www.auburn.edu/~bwm0005/sample.jpg > > However, price may be an issue. > > Any suggestions for a less expensive or free alternative which you think will suite my purposes would be greatly appreciated. > > > Sincerely, > > Billy > > > +++++++++++++++++++ > Billy Wayne McCann > Acevedo Research > Auburn University, Alabama > Office # = 334-844-6948 > +++++++++++++++++++ > -- Schrödinger Knowledge Base: http://www.schrodinger.com/kb/ Direct Support Phone: +49 (621) 438 55173 ---------------------------------------------------------------- Dr. Daniel Cappel - Senior Applications Scientist ---------------------------------------------------------------- Sitz der Gesellschaft/Registered Office: Schrödinger GmbH, Dynamostr. 13, D-68165 Mannheim Geschäftsführer/Managing Director:  Dr. Jörg Weiser Handelsregister/Commercial Register: HRB 9583 Amtsgericht Mannheim From owner-chemistry@ccl.net Wed Feb 15 11:44:01 2012 From: "Javier Cerezo jcb1~~um.es" To: CCL Subject: CCL:G: Molecular mechanics (and External keyword) in Gaussian and Redudant coordinates Message-Id: <-46297-120215071049-29122-pO9F6Lq7aPrkLhLhY2LoDg!A!server.ccl.net> X-Original-From: Javier Cerezo Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 15 Feb 2012 13:10:41 +0100 MIME-Version: 1.0 Sent to CCL by: Javier Cerezo [jcb1 . um.es] Hi all I am trying to use the "external" keyword in Gaussian09 to compute gradients with an external MM package. The goal is to use the Gaussian optimizer with redundant coordinates to perform a relaxed PES scan. Gradients are successfully communicated but when I use "ModRedundant" keyword, the redundant coordinates are simply ignored and a normal optimization is performed. Actually the following information is given in the log file (link103): "No Z-matrix variables, so optimization will use Cartesian coordinates." This is also the case when a one of the MM potentials implemented in Gaussian is used. I found no information about this issue in the Gaussian website nor in the ccl.net archives, so I wonder if some else has encounter this problem and if is there any possible workaround to make redundant coordinates work in such a case. Thanks Javier -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) From owner-chemistry@ccl.net Wed Feb 15 12:19:01 2012 From: "Arnout Voet Arnout.Voet{:}fys.kuleuven.be" To: CCL Subject: CCL: Creating "cartoony" molecular images Message-Id: <-46298-120214215112-30638-+GhX4eaWQ3iMthEwCRFPIQ_._server.ccl.net> X-Original-From: Arnout Voet Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 15 Feb 2012 02:50:57 +0000 MIME-Version: 1.0 Sent to CCL by: Arnout Voet [Arnout.Voet##fys.kuleuven.be] Dear Billy , You might want to take a look into pymol . If you tweak with following settings you should get something nice i first would turn of any shadows set ray_shadows, 0 set ray_trace_mode, 1 this will add the black lines around your molecules but the content is still glossy set ray_trace_mode, 2 this will just take the black lines and everything else is white, take a pencil and you could color it in yourself set ray_trace_mode, 3 this will take the black lines and non shine color inside more info on : http://www.pymolwiki.org/index.php/Ray by changing sphere and bond radius you might get what you are looking for. hope it can be any help of you kind regards Arnout ________________________________________ > From: owner-chemistry+arnout.voet==fys.kuleuven.be*_*ccl.net [owner-chemistry+arnout.voet==fys.kuleuven.be*_*ccl.net] on behalf of Billy McCann bwm0005() tigermail.auburn.edu [owner-chemistry*_*ccl.net] Sent: Wednesday, February 15, 2012 12:58 AM To: Arnout Voet Subject: CCL: Creating "cartoony" molecular images Sent to CCL by: Billy McCann [bwm0005 * tigermail.auburn.edu] Greetings All. I'm attempting to create molecular images which are very "cartoony" in nature, i.e. no lighting or shine on the atoms, bonds represented as thick black lines, etc. For example, see the following image linked below: http://www.auburn.edu/~bwm0005/sample2.jpg The software which was previously used is designed for an outdated platform (classic Mac) and so I'm searching for a replacement. I've tried many of the popular molecular imaging programs, but most create plastic and/or metallic looking images even after tweaking the settings. The product with which I've come closest is Chemcraft. I adjusted the configuration of the trial-ware version to produce the following image, which is very close to my goal: http://www.auburn.edu/~bwm0005/sample.jpg However, price may be an issue. Any suggestions for a less expensive or free alternative which you think will suite my purposes would be greatly appreciated. Sincerely, Billy +++++++++++++++++++ Billy Wayne McCann Acevedo Research Auburn University, Alabama Office # = 334-844-6948 +++++++++++++++++++http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Feb 15 12:54:00 2012 From: "Edward Holland hollandej*Cardiff.ac.uk" To: CCL Subject: CCL: Creating "cartoony" molecular images Message-Id: <-46299-120215031955-27463-943p0lG8lT2Wmd2K5i+QEA**server.ccl.net> X-Original-From: Edward Holland Content-Type: multipart/signed; boundary="Apple-Mail=_3D3EAAA0-1823-4CC8-BCA4-12F2A4391C56"; protocol="application/pgp-signature"; micalg=pgp-sha1 Date: Wed, 15 Feb 2012 08:19:41 +0000 Mime-Version: 1.0 (Apple Message framework v1251.1) Sent to CCL by: Edward Holland [hollandej a Cardiff.ac.uk] --Apple-Mail=_3D3EAAA0-1823-4CC8-BCA4-12F2A4391C56 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Macmolplt is free and creates "cartoony" looking atoms, this can = probably be further tweaked it the settings =20 On 14 Feb 2012, at 23:58, Billy McCann bwm0005() tigermail.auburn.edu = wrote: >=20 > Sent to CCL by: Billy McCann [bwm0005 * tigermail.auburn.edu] > Greetings All. >=20 > I'm attempting to create molecular images which are very "cartoony" in = nature, i.e. no lighting or shine on the atoms, bonds represented as = thick black lines, etc. >=20 > For example, see the following image linked below: > http://www.auburn.edu/~bwm0005/sample2.jpg >=20 > The software which was previously used is designed for an outdated = platform (classic Mac) and so I'm searching for a replacement. I've = tried many of the popular molecular imaging programs, but most create = plastic and/or metallic looking images even after tweaking the settings. = =20 >=20 > The product with which I've come closest is Chemcraft. I adjusted the = configuration of the trial-ware version to produce the following image, = which is very close to my goal: > http://www.auburn.edu/~bwm0005/sample.jpg >=20 > However, price may be an issue. >=20 > Any suggestions for a less expensive or free alternative which you = think will suite my purposes would be greatly appreciated. >=20 >=20 > Sincerely, >=20 > Billy >=20 >=20 > +++++++++++++++++++ > Billy Wayne McCann =20 > Acevedo Research > Auburn University, Alabama > Office # =3D 334-844-6948 > +++++++++++++++++++ >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 --Apple-Mail=_3D3EAAA0-1823-4CC8-BCA4-12F2A4391C56 Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename=signature.asc Content-Type: application/pgp-signature; name=signature.asc Content-Description: Message signed with OpenPGP using GPGMail -----BEGIN PGP SIGNATURE----- iQEcBAEBAgAGBQJPO2qdAAoJEEJc9s8gBQlybxkH/0gJQ646rYns3fHhnZRiJmyM 4RH8c0tMhAgdfIX4kEVLnvmwJaNo4HFieKrZ93CTbii/GGTUUpXgQZPVpnSB2wH4 219dkNhA/cmce9AqQp27S1L4kT96zx/8DwVXrJqtAxg6o5/MsqgVy0Rj5/Jw6CKb Eqyf23IYCChhPEbfvxs+AO0VfkQGBWwHg766PS5fli/q3vwxGc23yrGiGODKyntz tcRwR2S/b8TCgBBssvokSHptIPKgXvJKJF9vTQipbvwqwPs3MX7zls1gxre4Dovq UpFQfD1WSwnDJlZz4OMXyXWe1pJ6nKtDMZgBrbAJ2aT83+as/NOLRPyi8MFKjvk= =oTVy -----END PGP SIGNATURE----- --Apple-Mail=_3D3EAAA0-1823-4CC8-BCA4-12F2A4391C56-- From owner-chemistry@ccl.net Wed Feb 15 13:29:00 2012 From: "Emilio Gallicchio emilio[#]biomaps.rutgers.edu" To: CCL Subject: CCL: Creating "cartoony" molecular images Message-Id: <-46300-120215100814-2967-MnBHrtrGKrx3ioJ2o5B+3Q#server.ccl.net> X-Original-From: Emilio Gallicchio Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 15 Feb 2012 10:08:03 -0500 MIME-Version: 1.0 Sent to CCL by: Emilio Gallicchio [emilio-#-biomaps.rutgers.edu] Molscript (http://www.avatar.se/molscript/index.html) by Per Kraulis used to be very popular for creating molecular cartoons. Some sample illustrations from our own work can be seen in this paper (and many others): http://dx.doi.org/10.1016/j.jmb.2005.08.009 Molscript is a powerful tool, but it's unclear to me whether it remains in current use and it is being actively maintained. Maybe Per Kraulis would be willing to comment? Emilio --  Dr. Emilio Gallicchio  Director of High Performance Computing  BioMaPS Institute - Rutgers University  Wright-Rieman Laboratories Room 205  610 Taylor Rd.  Piscataway, NJ  08854-8087  Email: emilio : biomaps.rutgers.edu  WWW: http://hpcp.rutgers.edu/~emilio  Phone: 732-445-5157   Fax: 732-445-5958 On Tue, Feb 14, 2012 at 6:58 PM, Billy McCann bwm0005() tigermail.auburn.edu wrote: > > Sent to CCL by: Billy McCann [bwm0005 * tigermail.auburn.edu] > Greetings All. > > I'm attempting to create molecular images which are very "cartoony" in nature, i.e. no lighting or shine on the atoms, bonds represented as thick black lines, etc. > > For example, see the following image linked below: > http://www.auburn.edu/~bwm0005/sample2.jpg > > The software which was previously used is designed for an outdated platform (classic Mac) and so I'm searching for a replacement.  I've tried many of the popular molecular imaging programs, but most create plastic and/or metallic looking images even after tweaking the settings. > > The product with which I've come closest is Chemcraft.  I adjusted the configuration of the trial-ware version to produce the following image, which is very close to my goal: > http://www.auburn.edu/~bwm0005/sample.jpg > > However, price may be an issue. > > Any suggestions for a less expensive or free alternative which you think will suite my purposes would be greatly appreciated. > > > Sincerely, > > Billy > > > +++++++++++++++++++ > Billy Wayne McCann > Acevedo Research > Auburn University, Alabama > Office # = 334-844-6948 > +++++++++++++++++++>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > From owner-chemistry@ccl.net Wed Feb 15 14:04:01 2012 From: "Gustaf Olsson gustaf.olsson_-_lnu.se" To: CCL Subject: CCL: Creating "cartoony" molecular images Message-Id: <-46301-120215022718-17275-aK4FZLVdz8QrFu5qltcq7A|*|server.ccl.net> X-Original-From: Gustaf Olsson Content-Language: sv-SE Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Wed, 15 Feb 2012 07:57:17 +0100 MIME-Version: 1.0 Sent to CCL by: Gustaf Olsson [gustaf.olsson++lnu.se] Wow, we were looking for exactly the same thing last week! The example image displays exactly the idea we had! We played around a lot with different softwares and finally managed to produce "cartoonish" 2D structures without shades or flashy effects using one of my free favourites for Mac; UCSF Chimera, producing almost exactly what you have in your example! I will post the exact settings as soon as I'm at the office! Best regards // Gustaf Skickat frÃ¥n min iPhone 15 feb 2012 kl. 03:24 skrev "Billy McCann bwm0005() tigermail.auburn.edu" : > > Sent to CCL by: Billy McCann [bwm0005 * tigermail.auburn.edu] > Greetings All. > > I'm attempting to create molecular images which are very "cartoony" in nature, i.e. no lighting or shine on the atoms, bonds represented as thick black lines, etc. > > For example, see the following image linked below: > http://www.auburn.edu/~bwm0005/sample2.jpg > > The software which was previously used is designed for an outdated platform (classic Mac) and so I'm searching for a replacement. I've tried many of the popular molecular imaging programs, but most create plastic and/or metallic looking images even after tweaking the settings. > > The product with which I've come closest is Chemcraft. I adjusted the configuration of the trial-ware version to produce the following image, which is very close to my goal: > http://www.auburn.edu/~bwm0005/sample.jpg > > However, price may be an issue. > > Any suggestions for a less expensive or free alternative which you think will suite my purposes would be greatly appreciated. > > > Sincerely, > > Billy > > > +++++++++++++++++++ > Billy Wayne McCann > Acevedo Research > Auburn University, Alabama > Office # = 334-844-6948 > +++++++++++++++++++> > From owner-chemistry@ccl.net Wed Feb 15 14:39:00 2012 From: "Arne Dieckmann adieckma---googlemail.com" To: CCL Subject: CCL: Creating "cartoony" molecular images Message-Id: <-46302-120215030412-12433-/lelrDBian4OsxED/sa47A]=[server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Wed, 15 Feb 2012 00:04:00 -0800 Mime-Version: 1.0 (Apple Message framework v1257) Sent to CCL by: Arne Dieckmann [adieckma*googlemail.com] Hi Billy, you can achieve the desired representation using pymol. Here some settings that you could put in a pymol script: hide everything show sticks show spheres set stick_radius, .09 set sphere_scale, .18 set sphere_scale, .13, elem H set bg_rgb=[1, 1, 1] set stick_quality, 50 set sphere_quality, 4 color gray88, elem C color red, elem O color marine, elem N color gray99, elem H set stick_color, black set ray_trace_mode, 1 set ray_texture, 0 set antialias, 4 set ambient, 0.5 set spec_count, 50 set shininess, 200 set specular, 2 set reflect, .08 By playing around with some of these settings you will probably end up with what you are looking for. Cheers, Arne - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Dr. Arne Dieckmann Houk Research Lab | University of California, Los Angeles On Feb 14, 2012, at 3:58 PM, Billy McCann bwm0005() tigermail.auburn.edu wrote: > > Sent to CCL by: Billy McCann [bwm0005 * tigermail.auburn.edu] > Greetings All. > > I'm attempting to create molecular images which are very "cartoony" in nature, i.e. no lighting or shine on the atoms, bonds represented as thick black lines, etc. > > For example, see the following image linked below: > http://www.auburn.edu/~bwm0005/sample2.jpg > > The software which was previously used is designed for an outdated platform (classic Mac) and so I'm searching for a replacement. I've tried many of the popular molecular imaging programs, but most create plastic and/or metallic looking images even after tweaking the settings. > > The product with which I've come closest is Chemcraft. I adjusted the configuration of the trial-ware version to produce the following image, which is very close to my goal: > http://www.auburn.edu/~bwm0005/sample.jpg > > However, price may be an issue. > > Any suggestions for a less expensive or free alternative which you think will suite my purposes would be greatly appreciated. > > > Sincerely, > > Billy > > > +++++++++++++++++++ > Billy Wayne McCann > Acevedo Research > Auburn University, Alabama > Office # = 334-844-6948 > +++++++++++++++++++> > From owner-chemistry@ccl.net Wed Feb 15 15:14:00 2012 From: "Sten Nilsson Lill stenil]~[chalmers.se" To: CCL Subject: CCL:G: Creating "cartoony" molecular images Message-Id: <-46303-120215031751-19365-JtNA8j9XeB1A/V7pffb/hA|,|server.ccl.net> X-Original-From: Sten Nilsson Lill Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 15 Feb 2012 08:17:38 +0000 MIME-Version: 1.0 Sent to CCL by: Sten Nilsson Lill [stenil(a)chalmers.se] Dear Billy, have you looked at XYZViewer by Sven de Marothy in Siegbahn's group? http://www.physto.se/~sven/ It reads Jaguar, Gaussian files as well as pdb and xyz-formats, and as far as I know it's free to use. Hope that helps! /Sten Ph.D. Sten Nilsson Lill Dep. of Chemistry University of Gothenburg SE-412 96 Gothenburg, Sweden e-mail: stenil_._chem.gu.se Phone: +46-31 786 9103 Fax: +46-31-772 3840 ________________________________________ > From: owner-chemistry+stenil==chem.gu.se_._ccl.net [owner-chemistry+stenil==chem.gu.se_._ccl.net] on behalf of Billy McCann bwm0005() tigermail.auburn.edu [owner-chemistry_._ccl.net] Sent: Wednesday, February 15, 2012 12:58 AM To: Nilsson Lill, Sten Subject: CCL: Creating "cartoony" molecular images Sent to CCL by: Billy McCann [bwm0005 * tigermail.auburn.edu] Greetings All. I'm attempting to create molecular images which are very "cartoony" in nature, i.e. no lighting or shine on the atoms, bonds represented as thick black lines, etc. For example, see the following image linked below: http://www.auburn.edu/~bwm0005/sample2.jpg The software which was previously used is designed for an outdated platform (classic Mac) and so I'm searching for a replacement. I've tried many of the popular molecular imaging programs, but most create plastic and/or metallic looking images even after tweaking the settings. The product with which I've come closest is Chemcraft. I adjusted the configuration of the trial-ware version to produce the following image, which is very close to my goal: http://www.auburn.edu/~bwm0005/sample.jpg However, price may be an issue. Any suggestions for a less expensive or free alternative which you think will suite my purposes would be greatly appreciated. Sincerely, Billy +++++++++++++++++++ Billy Wayne McCann Acevedo Research Auburn University, Alabama Office # = 334-844-6948 +++++++++++++++++++http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Feb 15 15:48:01 2012 From: "Billy McCann bwm0005^^^tigermail.auburn.edu" To: CCL Subject: CCL: Creating "cartoony" molecular images Message-Id: <-46304-120215104204-1570-FgpsrE6QyLVUcmKZmnBtAA~~server.ccl.net> X-Original-From: Billy McCann Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 15 Feb 2012 15:41:42 +0000 MIME-Version: 1.0 Sent to CCL by: Billy McCann [bwm0005]![tigermail.auburn.edu] Thanks to those who responded. Some have contacted me directly due to problems encountered while trying to respond via CCL. The program which suites my needs perfectly is XYZviewer. http://www.physto.se/~sven/ It's java and so runs everywhere and is also free of charge. Billy +++++++++++++++++++ Billy Wayne McCann Acevedo Research Auburn University, Alabama Office # = 334-844-6948 +++++++++++++++++++ -----Original Message----- > From: owner-chemistry+bwm0005==auburn.edu]-[ccl.net [mailto:owner-chemistry+bwm0005==auburn.edu]-[ccl.net] On Behalf Of Billy McCann bwm0005() tigermail.auburn.edu Sent: Tuesday, February 14, 2012 5:59 PM To: Billy McCann Subject: CCL: Creating "cartoony" molecular images Sent to CCL by: Billy McCann [bwm0005 * tigermail.auburn.edu] Greetings All. I'm attempting to create molecular images which are very "cartoony" in nature, i.e. no lighting or shine on the atoms, bonds represented as thick black lines, etc. For example, see the following image linked below: http://www.auburn.edu/~bwm0005/sample2.jpg The software which was previously used is designed for an outdated platform (classic Mac) and so I'm searching for a replacement. I've tried many of the popular molecular imaging programs, but most create plastic and/or metallic looking images even after tweaking the settings. The product with which I've come closest is Chemcraft. I adjusted the configuration of the trial-ware version to produce the following image, which is very close to my goal: http://www.auburn.edu/~bwm0005/sample.jpg However, price may be an issue. Any suggestions for a less expensive or free alternative which you think will suite my purposes would be greatly appreciated. Sincerely, Billy +++++++++++++++++++ Billy Wayne McCann Acevedo Research Auburn University, Alabama Office # = 334-844-6948 +++++++++++++++++++http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Feb 15 16:23:01 2012 From: "Mikolaj Feliks mikolaj.feliks^^uni-bayreuth.de" To: CCL Subject: CCL: Creating "cartoony" molecular images Message-Id: <-46305-120215110438-26528-B4jnB1a3r92AZNFFflyiRw+/-server.ccl.net> X-Original-From: Mikolaj Feliks Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 15 Feb 2012 17:04:23 +0100 MIME-Version: 1.0 Sent to CCL by: Mikolaj Feliks [mikolaj.feliks-x-uni-bayreuth.de] Hi Billy, there is a program xmakemol for making cartoon-style images of molecules, in a postscript format: http://www.nongnu.org/xmakemol/ Only the problem is that they are ugly. But it's a matter of taste. Sincerely, mfx On 02/15/2012 12:58 AM, Billy McCann bwm0005() tigermail.auburn.edu wrote: > > Sent to CCL by: Billy McCann [bwm0005 * tigermail.auburn.edu] > Greetings All. > > I'm attempting to create molecular images which are very "cartoony" in nature, i.e. no lighting or shine on the atoms, bonds represented as thick black lines, etc. > > For example, see the following image linked below: > http://www.auburn.edu/~bwm0005/sample2.jpg > > The software which was previously used is designed for an outdated platform (classic Mac) and so I'm searching for a replacement. I've tried many of the popular molecular imaging programs, but most create plastic and/or metallic looking images even after tweaking the settings. > > The product with which I've come closest is Chemcraft. I adjusted the configuration of the trial-ware version to produce the following image, which is very close to my goal: > http://www.auburn.edu/~bwm0005/sample.jpg > > However, price may be an issue. > > Any suggestions for a less expensive or free alternative which you think will suite my purposes would be greatly appreciated. > > > Sincerely, > > Billy > > > +++++++++++++++++++ > Billy Wayne McCann > Acevedo Research > Auburn University, Alabama > Office # = 334-844-6948 > +++++++++++++++++++> > -- Mikolaj Feliks, M.Sc. Computational Biochemistry Group Universitätsstr. 30, B14 95447 Bayreuth Germany Tel.: +49-921-55-3078 e-mail: Mikolaj.Feliks()uni-bayreuth.de http://www.bisb.uni-bayreuth.de From owner-chemistry@ccl.net Wed Feb 15 16:58:01 2012 From: "ros rodrigogalindo__gmail.com" To: CCL Subject: CCL: Creating "cartoony" molecular images Message-Id: <-46306-120215123232-26828-AfekVybx4JLRcjO5vR2dCA++server.ccl.net> X-Original-From: ros Content-Type: multipart/alternative; boundary=f46d044785271d6e7704b9041840 Date: Wed, 15 Feb 2012 10:32:22 -0700 MIME-Version: 1.0 Sent to CCL by: ros [rodrigogalindo ~ gmail.com] --f46d044785271d6e7704b9041840 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Qutemol will provide lots of rendering options. It takes PDB files as input and has built in visualization templates. http://qutemol.sourceforge.net/ Hope it helps! Rodrigo. 2012/2/15 Daniel Cappel daniel.cappel() schrodinger.com < owner-chemistry|ccl.net> > > Sent to CCL by: Daniel Cappel [daniel.cappel!^!schrodinger.com] > Hi Billy! > > You should have a look at PyMOL, a user-sponsored open-source > visualization tool. > > www.pymol.org > > Therewith you can set different, so called, ray_trace_modes. This > allows you to create images with a cartoony appearance. For a few > examples have a look at this wiki page. > > http://www.pymolwiki.org/index.php/Ray#Modes > > Of course this also works for small molecules and not only for > proteins as shown in these examples. > > Best, Daniel > > On Wed, Feb 15, 2012 at 12:58 AM, Billy McCann bwm0005() > tigermail.auburn.edu wrote: > > > > Sent to CCL by: Billy McCann [bwm0005 * tigermail.auburn.edu] > > Greetings All. > > > > I'm attempting to create molecular images which are very "cartoony" in > nature, i.e. no lighting or shine on the atoms, bonds represented as thic= k > black lines, etc. > > > > For example, see the following image linked below: > > http://www.auburn.edu/~bwm0005/sample2.jpg > > > > The software which was previously used is designed for an outdated > platform (classic Mac) and so I'm searching for a replacement. I've trie= d > many of the popular molecular imaging programs, but most create plastic > and/or metallic looking images even after tweaking the settings. > > > > The product with which I've come closest is Chemcraft. I adjusted the > configuration of the trial-ware version to produce the following image, > which is very close to my goal: > > http://www.auburn.edu/~bwm0005/sample.jpg > > > > However, price may be an issue. > > > > Any suggestions for a less expensive or free alternative which you thin= k > will suite my purposes would be greatly appreciated. > > > > > > Sincerely, > > > > Billy > > > > > > +++++++++++++++++++ > > Billy Wayne McCann > > Acevedo Research > > Auburn University, Alabama > > Office # =3D 334-844-6948 > > +++++++++++++++++++ > > > > > -- > Schr=F6dinger Knowledge Base: http://www.schrodinger.com/kb/ > Direct Support Phone: +49 (621) 438 55173 > > ---------------------------------------------------------------- > > Dr. Daniel Cappel - Senior Applications Scientist > > ---------------------------------------------------------------- > Sitz der Gesellschaft/Registered Office: > Schr=F6dinger GmbH, Dynamostr. 13, D-68165 Mannheim > Gesch=E4ftsf=FChrer/Managing Director: Dr. J=F6rg Weiser > Handelsregister/Commercial Register: HRB 9583 Amtsgericht Mannheim > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --f46d044785271d6e7704b9041840 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Qutemol will provide lots of rendering options. It takes PDB files as input= and has built in visualization templates.

http://qutemol.sourceforge.net/

Hope it helps= !

Rodrigo.

2012/2/15 Daniel Cappel dani= el.cappel() schrodinger.com <owner-chemistry|cc= l.net>

Sent to CCL by: Daniel Cappel [daniel.cappel!^!schrodinger.com]
Hi Billy!

You should have a look at PyMOL, a user-sponsored open-source
visualization tool.

www.pymol.org

Therewith you can set different, so called, ray_trace_modes. This
allows you to create images with a cartoony appearance. For a few
examples have a look at this wiki page.

= http://www.pymolwiki.org/index.php/Ray#Modes

Of course this also works for small molecules and not only for
proteins as shown in these examples.

Best, Daniel

On Wed, Feb 15, 2012 at 12:58 AM, Billy McCann bwm0005()
tigermail.auburn.= edu <owner-chemistry*_*= ccl.net> wrote:
>
> Sent to CCL by: Billy McCann [bwm0005 * tigermail.auburn.edu]
> Greetings All.
>
> I'm attempting to create molecular images which are very "car= toony" in nature, i.e. no lighting or shine on the atoms, bonds repres= ented as thick black lines, etc.
>
> For example, see the following image linked below:
> http://www.auburn.edu/~bwm0005/sample2.jpg
>
> The software which was previously used is designed for an outdated pla= tform (classic Mac) and so I'm searching for a replacement. =A0I've= tried many of the popular molecular imaging programs, but most create plas= tic and/or metallic looking images even after tweaking the settings.
>
> The product with which I've come closest is Chemcraft. =A0I adjust= ed the configuration of the trial-ware version to produce the following ima= ge, which is very close to my goal:
> http://www.auburn.edu/~bwm0005/sample.jpg
>
> However, price may be an issue.
>
> Any suggestions for a less expensive or free alternative which you thi= nk will suite my purposes would be greatly appreciated.
>
>
> Sincerely,
>
> Billy
>
>
> +++++++++++++++++++
> Billy Wayne McCann
> Acevedo Research
> Auburn University, Alabama
> Office # =3D 334-8= 44-6948
> +++++++++++++++++++
>


--
Schr=F6dinger Knowledge Base: http://www.schrodinger.com/kb/
Direct Support Phone: +49 (621) 438 55173

----------------------------------------------------------------

Dr. Daniel Cappel - Senior Applications Scientist

----------------------------------------------------------------
Sitz der Gesellschaft/Registered Office:
Schr=F6dinger GmbH, Dynamostr. 13, D-68165 Mannheim
Gesch=E4ftsf=FChrer/Managing Director:=A0 Dr. J=F6rg Weiser
Handelsregister/Commercial Register: HRB 9583 Amtsgericht Mannheim



-=3D This is automatically added to each message by the mailing script =3D-=
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--f46d044785271d6e7704b9041840-- From owner-chemistry@ccl.net Wed Feb 15 17:33:01 2012 From: "Elaine Meng meng~!~cgl.ucsf.edu" To: CCL Subject: CCL: Creating "cartoony" molecular images Message-Id: <-46307-120215122820-17339-9gb7/NdBnW6V+dBNkavomg^^^server.ccl.net> X-Original-From: "Elaine Meng" Date: Wed, 15 Feb 2012 12:28:19 -0500 Sent to CCL by: "Elaine Meng" [meng{}cgl.ucsf.edu] Hi Billy, It can also be done pretty easily in Chimera, with a few display options. These options can be set in dialogs or in Chimera commands, for example: open pubchem:12123 preset apply pub 1 light mode ambient represent bs bondcolor black set silhouette_width 3 setattr m stickScale .3 That doesn't include the element labels. It might be difficult to place the regular (3D) labels that move along with the structure centered exactly on the balls, but it could be done easily with 2D Labels once you have your final view. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Wed Feb 15 18:08:00 2012 From: "Francisco Hernandez-Guzman Francisco.Hernandez^accelrys.com" To: CCL Subject: CCL: Creating "cartoony" molecular images Message-Id: <-46308-120215151719-29174-MzPk3z0OIHCwaERTS/Lbxg:-:server.ccl.net> X-Original-From: Francisco Hernandez-Guzman Content-Language: en-US Content-Type: multipart/related; boundary="_004_55AC410F3302E740AC9EC50011F73E8F041952DACFEXCH1COLOacce_"; type="multipart/alternative" Date: Wed, 15 Feb 2012 12:16:51 -0800 MIME-Version: 1.0 Sent to CCL by: Francisco Hernandez-Guzman [Francisco.Hernandez]~[accelrys.com] --_004_55AC410F3302E740AC9EC50011F73E8F041952DACFEXCH1COLOacce_ Content-Type: multipart/alternative; boundary="_000_55AC410F3302E740AC9EC50011F73E8F041952DACFEXCH1COLOacce_" --_000_55AC410F3302E740AC9EC50011F73E8F041952DACFEXCH1COLOacce_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Billy, Another alternative can be using our free DS Visualizer. http://accelrys.co= m/products/discovery-studio/visualization-download.php With minimal UI driven adjustments to you can easily create an image like t= his one. [cid:image003.jpg:01CCEBDB.B2AA9270] Cheers, Francisco Sr. Product Manager http://accelrys.com -----Original Message----- > From: owner-chemistry+francisco.hernandez=3D=3Daccelrys.com:ccl.net [mailto= :owner-chemistry+francisco.hernandez=3D=3Daccelrys.com:ccl.net] On Behalf O= f Billy McCann bwm0005() tigermail.auburn.edu Sent: Tuesday, February 14, 2012 3:59 PM To: Francisco Hernandez-Guzman Subject: CCL: Creating "cartoony" molecular images Sent to CCL by: Billy McCann [bwm0005 * tigermail.auburn.edu] Greetings All= . I'm attempting to create molecular images which are very "cartoony" in natu= re, i.e. no lighting or shine on the atoms, bonds represented as thick blac= k lines, etc. For example, see the following image linked below: http://www.auburn.edu/~bwm0005/sample2.jpg The software which was previously used is designed for an outdated platform= (classic Mac) and so I'm searching for a replacement. I've tried many of = the popular molecular imaging programs, but most create plastic and/or meta= llic looking images even after tweaking the settings. The product with which I've come closest is Chemcraft. I adjusted the conf= iguration of the trial-ware version to produce the following image, which i= s very close to my goal: http://www.auburn.edu/~bwm0005/sample.jpg However, price may be an issue. Any suggestions for a less expensive or free alternative which you think wi= ll suite my purposes would be greatly appreciated. Sincerely, Billy +++++++++++++++++++ Billy Wayne McCann Acevedo Research Auburn University, Alabama Office # =3D 334-844-6948 +++++++++++++++++++ -=3D This is automatically added to each message by the mailing script =3D-=t= he strange characters on the top line to the : sign. You can also look up t= he X-Original-From: line in the mail header. E-mail to subscribers: CHEMISTRY:ccl.net or use:E-mail to administrators: CHEMISTRY-REQUEST:ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_55AC410F3302E740AC9EC50011F73E8F041952DACFEXCH1COLOacce_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi Billy,

 

Another alternative can be using our free DS Visualizer. htt= p://accelrys.com/products/discovery-studio/visualization-download.php

 

With minimal UI driven adjustments to you can easily create an image= like this one.

 

=

 

Cheers,

 

Francisco

 

=

Sr. Product Manager

http://accelrys.com

 

 

-----Original Message-----
From= : owner-chemistry+francisco.hernandez=3D=3Daccelrys.com:ccl.net [mailto:own= er-chemistry+francisco.hernandez=3D=3Daccelrys.com:ccl.net] On Behalf Of Bi= lly McCann bwm0005() tigermail.auburn.edu
Sent: Tuesday, February 14, 20= 12 3:59 PM
To: Francisco Hernandez-Guzman
Subject: CCL: Creating &quo= t;cartoony" molecular images

 

 

Sent to CCL by: Billy McCann [bwm0005 * tigermail.auburn.edu] Greetings Al= l.

 

I'm attempting to create molecular images which are very "c= artoony" in nature, i.e. no lighting or shine on the atoms, bonds repr= esented as thick black lines, etc.

 

For example, see the following i= mage linked below:

http://www.auburn.edu/~bwm0005/sample2.jpg<= /o:p>

 

The software which was previously used is designed for an outdated platf= orm (classic Mac) and so I'm searching for a replacement.  I've tried = many of the popular molecular imaging programs, but most create plastic and= /or metallic looking images even after tweaking the settings. 

 

The product with which I've come closest is Chemcraft.  I adjusted t= he configuration of the trial-ware version to produce the following image, = which is very close to my goal:

http://www.auburn.edu/~bwm0005/sample.jpg

 

However, price may be an issue.

 

Any suggestions for= a less expensive or free alternative which you think will suite my purpose= s would be greatly appreciated.

=  

 

Sincerely,

 

Billy

 

 

+++++++++++++++++++

Bill= y Wayne McCann      

Acevedo Research

Aubu= rn University, Alabama

Office # =3D 3= 34-844-6948

+++++++++++++++++++<= /o:p>

 

 

 

-=3D This is automatically added to each message by the m= ailing script =3D- To recover the email address of the author of the messag= e, please change the strange characters on the top line to the : sign. You = can also

 

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 =

 

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From owner-chemistry@ccl.net Wed Feb 15 20:17:01 2012 From: "Marc Segovia marc^fq.edu.uy" To: CCL Subject: CCL:G: running Gaussrate on VRC polyrate Message-Id: <-46309-120215174029-13389-yw8hR3V2ZxXarDhwHrdAMw * server.ccl.net> X-Original-From: Marc Segovia Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 16 Feb 2012 20:37:43 -0200 MIME-Version: 1.0 Sent to CCL by: Marc Segovia [marc/a\fq.edu.uy] Hi I install polyrate on my PC, VRC variant (barrierless reactions), run ch3 tutorial , put when I try to move to gaussrate (where cannot found a sample) , I have problems, with connection between gaussrate and gaussian, even that shuttle was properly modified, and esp.fu7* files runs perfect on gaussian. The following message appear Error opening the file esp.fu71 which is linked to FORTRAN unit 71 Error opening the file esp.fu72 which is linked to FORTRAN unit 72 Error opening the file esp.fu73 which is linked to FORTRAN unit 73 Could someone give me a hint or a sample. Thanking in advances Best Regards Marc Dr. Marc Segovia CCBG-DETEMA Facultad de Quimica Universidad de la Republica 11700 Montevideo Uruguay