From owner-chemistry@ccl.net Tue Feb 14 08:02:00 2012 From: "Roger Robinson scu98rkr+/-gmail.com" To: CCL Subject: CCL: Good Vibrations Message-Id: <-46284-120214074958-25212-039jAoceO7lTQNhHDj/6YA[*]server.ccl.net> X-Original-From: Roger Robinson Content-Type: multipart/alternative; boundary="------------050702050201040908010502" Date: Tue, 14 Feb 2012 12:50:12 +0000 MIME-Version: 1.0 Sent to CCL by: Roger Robinson [scu98rkr]|[gmail.com] This is a multi-part message in MIME format. --------------050702050201040908010502 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit 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) --------------050702050201040908010502 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit 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)
--------------050702050201040908010502-- From owner-chemistry@ccl.net Tue Feb 14 12:02:01 2012 From: "Andras Borosy andras.borosy##givaudan.com" To: CCL Subject: CCL: Good Vibrations Message-Id: <-46285-120214092026-25329-49pAKjjcqCde0untkivoaA(0)server.ccl.net> X-Original-From: Andras Borosy Content-Type: multipart/alternative; boundary="=_alternative 004EBA7EC12579A4_=" Date: Tue, 14 Feb 2012 15:19:53 +0100 MIME-Version: 1.0 Sent to CCL by: Andras Borosy [andras.borosy[#]givaudan.com] This is a multipart message in MIME format. --=_alternative 004EBA7EC12579A4_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Great, I like it and Beach Boys, too! Regrads, Andr=E1s Borosy > From: "Roger Robinson scu98rkr+/-gmail.com" To: "Borosy, Andras " Date: 14.02.2012 15:17 Subject: CCL: Good Vibrations Sent by: owner-chemistry+andras.borosy=3D=3Dgivaudan.com _ ccl.net Hi All, While working today "Good Vibrations" by the Beach boys came on in the=20 background on Last.fm. Has it ever occured to anyone that Good Vibrations might be about the=20 formation of Excited states and the vibrational frequencies seen in=20 emission spectra of molecules ? Explanation below. Roger Ah! I love the colorful clothes she wears (she's the atom and he's=20 interested in the vibration frequencies (colours) produced by emission)=20 And the way the sunlight plays upon her hair (UV light shone upon atom.=20 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=20 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=20 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) --=_alternative 004EBA7EC12579A4_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Great, I like it and Beach Boys, too!

Regrads,

 Andr=E1s Borosy




From:     =    "Roger Robinson scu98rkr+/-gmail.com" <owner-chemistry _ ccl.net>
To:     &n= bsp;  "Borosy, Andras " <andras.borosy _ givaudan.com>
Date:     =    14.02.2012 15:17
Subject:   &nbs= p;    CCL: Good Vibrations=
Sent by:   &nbs= p;    owner-chemistry+andr= as.borosy=3D=3Dgivaudan.com _ ccl.net




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 forma= tion 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 inter= ested in the vibration frequencies (colours) produced by emission)
And the way the sunlight plays upon her hair (UV light shone upon atom.<= /b> 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)

--=_alternative 004EBA7EC12579A4_=-- From owner-chemistry@ccl.net Tue Feb 14 12:37:01 2012 From: "sergio.manzetti[]gmail.com" To: CCL Subject: CCL: Good Vibrations Message-Id: <-46286-120214090701-3957-/ZZR8PJ1rFaatSBWR74oTA,+,server.ccl.net> X-Original-From: sergio.manzetti[#]gmail.com Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Tue, 14 Feb 2012 15:06:49 +0100 MIME-Version: 1.0 Sent to CCL by: sergio.manzetti[-]gmail.com Haha! That was a good one! > ----- Original Message ----- > From: Roger Robinson scu98rkr+/-gmail.com > Sent: 02/14/12 01:50 PM > To: Manzetti, Sergio > Subject: CCL: Good Vibrations > > 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) > From owner-chemistry@ccl.net Tue Feb 14 16:06:01 2012 From: "Joe Corkery jcorkery.:.eyesopen.com" To: CCL Subject: CCL: OpenEye CUP XIII - Final Agenda / Poster Presentations Still Welcome Message-Id: <-46287-120214160415-9079-Y9hWNwgDdo39wiKgbKz+LQ\a/server.ccl.net> X-Original-From: Joe Corkery Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_CB603671ECF9jcorkeryeyesopencom_" Date: Tue, 14 Feb 2012 13:04:01 -0800 MIME-Version: 1.0 Sent to CCL by: Joe Corkery [jcorkery|-|eyesopen.com] --_000_CB603671ECF9jcorkeryeyesopencom_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Colleagues, The final agenda for OpenEye's 13th annual CUP meeting is now available and= can be seen below. The meeting will be held March 5-7, 2012 at the Eldorad= o Hotel & Spa in Santa Fe, NM. Professor Johnny Gasteiger will give the Lev= inthal keynote lecture. In addition to the main sessions, there will be a s= pecial pre-meeting session on toolkit programming Sunday afternoon (March 4= th) as well as a training program the previous Thursday and Friday (March 1= -2). The conference, as always, does not have a registration fee, but we do= ask you to register. We do hope that you will join us for what promises to= be one of the best CUP meetings yet. Poster submissions are still welcome = and can be made when registering. http://www.eyesopen.com/events/cup13 Levinthal Lecture * Johnny Gasteiger, University of Erlangen-N=FCrnberg Main Sessions Proteins: What information should we look for? * James Fraser, UCSF - "Some like it hot: Protein Conformational Ensembl= es by X-ray Crystallography" * Vijay Pande, Stanford University - "New approaches to conformational s= ampling of peptides" * Michael Wall, Los Alamos National Labs - "Protein Dynamics and Diffuse= X-ray Scattering" * Greg Warren, OpenEye - TBA * Lauren Webb, University of Texas - "Exploring Electrostatic Fields at = the Protein-Protein Interface" Myths in Modeling * Colin Groom, CCDC - TBA * Ajay Jain, UCSF - "Myth: You showed your method "works" so it must WOR= K!" * Anthony Nicholls, OpenEye - TBA * Tudor Oprea, University of New Mexico - "Myths and half-truths I've di= scovered while practicing cheminformatics" * Jeremy Tame, Yokohama University - "Some thoughts on scoring functions= " Shape & Electrostatics * Andrew Grant, AstraZeneca - TBA * Andrew Good, Genzyme - "Fragment fat wobbles too: Implications of prom= iscuous Pim-1 kinase fragment inhibitor hydrophobic interactions for FBDD" * Paul Hawkins, OpenEye - TBA * Dave Mobley, University of New Orleans - "Free energy calculations usi= ng MD: Is that like free lunch?" * Mike Word, OpenEye - TBA To Affinity and beyond: How important is solubility? * Carleton Sage, Arena - "Solubility in the Context of the Clinical Cand= idate Manifold" * Dan Ortwine, Genentech - TBA * Steve Johnson, Bristol-Myers Squibb - TBA * Discussion chaired by Kent Stewart, Abbott Labs New Things to Consider * Mike Schnieders, Univesity of Texas - "Pharmaceutical Applications of = the Polarizable AMOEBA Force Field" * Yibing Shan, D. E. Shaw - "How Does a Drug Molecule Find Its Target Bi= nding Site in Src Kinase" * Colin Stultz, MIT - TBA * Shun Zhu, University of Iowa - "Accurate prediction of mutational effe= cts on the thermodynamics of inhibitor binding to p38alpha MAP kinsase: dir= ect comparison of simulation with experiment" Cloud Computing * Greg Bakken, Pfizer - "So This is the Cloud ... Now What?" * Jose Duca, Novartis - "Reflecting on ways to use the cloud in drug dis= covery and the importance of the scientist's current address" * Scott Le Grand, Amazon - TBA * Vijay Pande, Stanford University - "So you've got $10,000 - what can A= mazon EC2 (or the equivalent) get you in terms of improving accuracy or pre= cision?" * Bob Tolbert, OpenEye - "Spinning your own cluster in the cloud: Cost, = Security and Performance" Toolkit Session (Sunday March 4th) * Krisztina Boda, OpenEye - "The Art of Chemistry" * Craig Bruce, OpenEye - "Keepalive with OEChem 24x7x365" * Ed Cannon, OpenEye - "Lexichem, a New Era" * Brian Cole, OpenEye - "Toolkit State of the Union" * Andrew Dalke, Dalke Scientific - "Working with PubChem-sized data from= home" * Matt Stahl, OpenEye - "The OpenEye Oracle Cartridge" * Pat Walters, Vertex - "OEChem everywheah - further adventures in integ= ration" --_000_CB603671ECF9jcorkeryeyesopencom_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
=

Dear Colleagues,

 =

The final agenda fo= r OpenEye's 13th annual CUP meeting is now available and can be seen below.= The meeting will be held March 5-7, 2012 at the Eldorado Hotel & Spa i= n Santa Fe, NM. Professor Johnny Gasteiger = will give the Levinthal keynote lecture. In addition to the main sessions, there will be a = special pre-meeting session on toolkit programming Sunday afternoon (March = 4th) as well as a training program the previous Thursday and Friday (March = 1-2). The conference, as always, does not have a registration fee, but we d= o ask you to register. We do hope that you will join us for what promises t= o be one of the best CUP meetings yet. Poster submissions are still welcome= and can be made when registering.

 

Levinthal Lecture

  • Johnny Gasteiger, University= of Erlangen-N=FCrnberg

Main Sessions=

Proteins: What information sh= ould we look for?

  • James Fraser, UCSF - "Some like it hot: Protein Conform= ational Ensembles by X-ray Crystallography"
  • Vijay Pande, Stanford Universi= ty - "New approaches to conformational sampling of peptides"
  • Michael Wall,= Los Alamos National Labs - "Protein Dynamics and Diffuse X-ray Scattering"=
  • Lauren Webb, University of Texas - "Exploring= Electrostatic Fields at the Protein-Protein Interface"

Myths in Modeling

<= ul type=3D"disc" style=3D"margin-bottom: 0in; ">
  • Colin Groom, CCDC - TBA
  • Ajay Jain, UCSF - "Myth= : You showed your method "works" so it must WORK!"Anthony Nicholls, OpenE= ye - TBA
  • Tudor Oprea, University of New Mexico - "Myths and half-truths I'= ve discovered while practicing cheminformatics"
  • Jeremy Tame, Yokohama Univ= ersity - "Some thoughts on scoring functions"
  • Sh= ape & Electrostatics

  • Andrew Grant, AstraZeneca - TBA=
  • Andrew Good, Gen= zyme - "Fragment fat wobbles too: Implications of promiscuous Pim-1 kinase = fragment inhibitor hydrophobic interactions for FBDD"
  • Paul Hawkins, OpenEy= e - TBA
  • Dave Mobley, University of New Orleans - "Free energy calculations= using MD: Is that like free lunch?"
  • Mike Word, OpenEye - TBA
  • = To Affinity and beyond: How important is solubility?<= /em>

    • Carlet= on Sage, Arena - "Solubility in the Context of the Clinical Candidate Manif= old"
    • Dan Ortwine, Genentech - TBA
    • Steve Johnson, Bristol-Myers Squibb - T= BA
    • Discussion chaired by Kent Stewart, Abbott Labs
    • <= /ul>

      New Things to Consider

      =
      • Mike Schnieders, Univesity of Texas - "Pharmace= utical Applications of the Polarizable AMOEBA Force Field"
      • Yibing Shan, D.= E. Shaw - "How Does a Drug Molecule Find Its Target Binding Site in Src Ki= nase"
      • Colin Stultz, MIT - TBA
      • Shun Zhu, University of Iowa - "Accurate pr= ediction of mutational effects on the thermodynamics of inhibitor binding t= o p38alpha MAP kinsase: direct comparison of simulation with experiment"

      Cloud Computing

      • Greg Bakken, Pfizer - "So This is= the Cloud ... Now What?"
      • Jose Duca, Novartis - "Reflecting on ways to use= the cloud in drug discovery and the importance of the scientist's current = address"
      • Scott Le Grand, Amazon - TBA
      • Vijay Pande, Stanford University - = "So you've got $10,000 - what can Amazon EC2 (or the equivalent) get you in= terms of improving accuracy or precision?"
      • Bob Tolbert, OpenEye - "Spinni= ng your own cluster in the cloud: Cost, Security and Performance"

      <= strong>Toolkit Session (Sunday March 4th)

      • Krisztina Bod= a, OpenEye - "The Art of Chemistry"
      • Craig Bruce, OpenEye - "Keepalive with= OEChem 24x7x365"
      • Ed Cannon, OpenEye - "Lexichem, a New Era"
      • Brian Cole, = OpenEye - "Toolkit State of the Union"
      • Andrew Dalke, Dalke Scientific - "W= orking with PubChem-sized data from home"
      • Matt Stahl, OpenEye - "The Ope= nEye Oracle Cartridge"
      • Pat Walters, Vertex - "OEChem everywheah - further= adventures in integration"

     

    --_000_CB603671ECF9jcorkeryeyesopencom_-- From owner-chemistry@ccl.net Tue Feb 14 17:44:00 2012 From: "Soaring Bear soaringbear ~~ yahoo.com" To: CCL Subject: CCL: Open Source Toxicity Prediction and QSAR Software Message-Id: <-46288-120214173858-23643-A5aO49yzNR1jkDlX0mICEg]-[server.ccl.net> X-Original-From: Soaring Bear Content-Type: text/plain; charset=us-ascii Date: Tue, 14 Feb 2012 14:38:52 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Soaring Bear [soaringbear#yahoo.com] see: http://www.ncbi.nlm.nih.gov/pubmed/22063083 Soaring Bear Ph.D. Pharmacology soaringbear at yahoo.com http://soaringbear.tripod.com/nature/WeedsforNeeds.html http://www.nlm.nih.gov/mesh/presentations/bear_2005_aug/index.htm author of http://HerbMed.org --- On Mon, 2/6/12, Arindam Ganguly arindamganguly(~)gmail.com wrote: > I am seeking information on OpenSource Software available > for Toxicity > prediction, preferably with a GUIs and on Windows Platform. > I guess, the > software will accept a chemical structure and utilize QSAR > for predicting > toxicity and compare it with published experimental results. From owner-chemistry@ccl.net Tue Feb 14 20:14:00 2012 From: "kiran kumar nalla kiran.nalla1984]~[gmail.com" To: CCL Subject: CCL:G: computational error Message-Id: <-46289-120214183010-10165-DMRhehuD5J41tA861Usb5Q_+_server.ccl.net> X-Original-From: "kiran kumar nalla" Date: Tue, 14 Feb 2012 18:30:08 -0500 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.com From owner-chemistry@ccl.net Tue Feb 14 20:49:00 2012 From: "Billy McCann bwm0005() tigermail.auburn.edu" To: CCL Subject: CCL: Creating "cartoony" molecular images Message-Id: <-46290-120214185931-21908-oTvewc81qBCHV0axG72MNQ|,|server.ccl.net> X-Original-From: Billy McCann Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 14 Feb 2012 23:58:58 +0000 MIME-Version: 1.0 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 +++++++++++++++++++