From owner-chemistry@ccl.net Mon Sep 17 00:21:01 2007 From: "Hans Martin Senn senn[-]chem.gla.ac.uk" To: CCL Subject: CCL: Orbitals/cube/Mac OS X Message-Id: <-35168-070916211719-8939-lmrbvm0SFhg9rl5JRrhccQ_._server.ccl.net> X-Original-From: Hans Martin Senn Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Mon, 17 Sep 2007 01:41:16 +0100 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Hans Martin Senn [senn-x-chem.gla.ac.uk] Hi Frank All of the below work and can produce nice-looking output. Your choice is mainly a question of personal taste and what other features you require the program to have. Cheers Hans VMD (http://www.ks.uiuc.edu/Research/vmd/) Molekel (http://www.bioinformatics.org/molekel/wiki/) Molden (requires X11; use OpenGL mode to get nice isosurfaces; http:// www.cmbi.ru.nl/molden/molden.html) gOpenMol (requires X11; http://www.csc.fi/gopenmol/index.phtml; or > from fink, http://fink.sf.net/) On 16 Sep 2007, at 17:07, Frank Neese neese%a%thch.uni-bonn.de wrote: > Sent to CCL by: Frank Neese [neese .. thch.uni-bonn.de] > Dear CCL'ers, > > i would greatly appreciate pointers to appropriate (preferably > free) software that allows visualization of molecules structures > *and* orbitals/densities on Mac OS X versions 10.4 and higher. The > input data may either be cube files or provided by appropriate > interfaces. So far, all of my (limited) attempts have failed - > there are many nice molecule viewers around but so far i have not > found a program that is easy to use and nicely visualizes cube > format data. If somebody knows a nice program that accepts the same > data in another well documented format - please let me know as well. > > All the best and many thanks in advance, > Frank From owner-chemistry@ccl.net Mon Sep 17 02:05:01 2007 From: "Satyan Sharma satyan _ sun3.oulu.fi" To: CCL Subject: CCL: IRC calculation Message-Id: <-35169-070917020317-19568-tMzFEfjrpd8pX5/cyyFrpg^^^server.ccl.net> X-Original-From: "Satyan Sharma" Date: Mon, 17 Sep 2007 02:03:14 -0400 Sent to CCL by: "Satyan Sharma" [satyan!A!sun3.oulu.fi] Dear CClers, I am trying to an IRC calculation. I have confirmed the TS using Freq calculation: * output from Freq: Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), depolarization ratios for plane and unpolarized incident light, reduced masses (AMU), force constants (mDyne/A), and normal coordinates: 1 2 3 A A A Frequencies -- -158.6525 16.8447 20.1106 Red. masses -- 14.3275 5.8131 7.0497 After this I tried to do IRC * Output from IRC: Z66 0.00104 0.00073 0.00160 -0.00034 -0.00076 X66 Y66 Z66 X66 0.28938 Y66 -0.07623 0.04939 Z66 -0.11068 0.04111 0.11344 ANGLE THETA= 93.10860 BRACKET FOR LAMBDA OBTAINED IN CYCLES= 99 Arithmetic Exception real 33:52.86 user 2:14:30.35 sys 31.52 Any suggestions. The Calculation crashes in the very first step. Regards, Satyan From owner-chemistry@ccl.net Mon Sep 17 03:15:00 2007 From: "Vlad vvv900{}anusf.anu.edu.au" To: CCL Subject: CCL:G: Geomview Message-Id: <-35170-070916231517-27493-S2Vr3CvhRXlKBoA0eyvlgQ : server.ccl.net> X-Original-From: Vlad Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1251; format=flowed Date: Mon, 17 Sep 2007 12:07:16 +1000 MIME-Version: 1.0 Sent to CCL by: Vlad [vvv900()anusf.anu.edu.au] Dear Tom, > I am new relatively new to the field of comp. chemestry. I want to use the program geomview to visualise the solvent cavity as created by the PCM model. You might want to have a look at the JMolEditor (http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html) which supports Gaussian input and output files as well as the OFF file format produced by Gaussian for PCM calculation. Gaussian produces two OFF files, tesserae.off and charge.off. You can download the molecule first and then the surface using the menu command "File"->"Load Graphics Object"->"off File". Later you can play with the opacity of your surface using command "View"->"Manage Objects". Best wishes, Vlad -- =============================== Dr. Vladislav Vassiliev Supercomputer Facility, ANU Canberra, ACT, 0200, Australia Phone: +61 2 6125-9694 Fax: +61 2 6125-8199 From owner-chemistry@ccl.net Mon Sep 17 05:29:01 2007 From: "Noel O Boyle baoilleach++gmail.com" To: CCL Subject: CCL:G: Eigenvectors and Eigenvalues of the overlap matrix of G03 Message-Id: <-35171-070917045857-26716-Zbt/rYkIoXpbperNZJy7bQ]-[server.ccl.net> X-Original-From: "Noel O Boyle" Date: Mon, 17 Sep 2007 04:58:53 -0400 Sent to CCL by: "Noel O Boyle" [baoilleach::gmail.com] Why not just calculate them yourself? With the right libraries, it's just 5 lines of code. (1) Install Python (2) Install Numeric - among other things, this provides an interface to LAPACK for linear algebra (3) Install cclib (http://cclib.sf.net) - this extracts information from computational chemistry output files - see http://dx.doi.org/10.1002/jcc.20823 (4) Here's a Python program to do it all for you: import LinearAlgebra > from cclib.parser import ccopen p = ccopen("mygaussianlogfile.log") p.parse() evalues, evectors = LinearAlgebra.eigenvectors(p.aooverlaps) Regards, Noel O'Boyle In reply to: Sent to CCL by: "Aggelos Avramopoulos" [aggavramop ~~ yahoo.gr] Dear CCLs I am using G03 and i would like to print out the eigenvectors and eigenvalues of the overlap matrix. I found that by using the option IOP(3/33=1) i can print in the produced rwf file the overlap matrix. Is there any way to print either in the log file or in any produced G03 file,the eigenvectors and the eigenvalues of the diagonilized overlap matrix? Or, alternatively since i know the overlap matrix, although not in a symmetric form, is there anyone who could provide either a code or any relevant software in order to diagonilize the matrix and to take the eigenvectors and the corresponding eigenvalues ? Thanks in advance for any help,hints and suggestions. Aggelos Avramopoulos From owner-chemistry@ccl.net Mon Sep 17 06:07:01 2007 From: "Jens Thomas j.m.h.thomas::dl.ac.uk" To: CCL Subject: CCL: Orbitals/cube/Mac OS X Message-Id: <-35172-070917060213-2098-7W38XYwnDiOJaDtfvz063w#server.ccl.net> X-Original-From: Jens Thomas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 17 Sep 2007 11:01:55 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Thomas [j.m.h.thomas]-[dl.ac.uk] Dear Frank, Frank Neese neese%a%thch.uni-bonn.de wrote: > > Sent to CCL by: Frank Neese [neese .. thch.uni-bonn.de] > Dear CCL'ers, > > i would greatly appreciate pointers to appropriate (preferably free) > software that allows visualization of molecules structures *and* > orbitals/densities on Mac OS X versions 10.4 and higher. The input > data may either be cube files or provided by appropriate interfaces. > So far, all of my (limited) attempts have failed - there are many nice > molecule viewers around but so far i have not found a program that is > easy to use and nicely visualizes cube format data. If somebody knows > a nice program that accepts the same data in another well documented > format - please let me know as well. The CCP1GUI should do what you want: http://www.cse.scitech.ac.uk/ccg/software/ccp1gui/ There are some screen shots of some of the sorts of visualisations that it can do at: http://sourceforge.net/project/screenshots.php?group_id=138504&ssid=65493 Best wishes, Jens -- =================================================================== Jens Thomas, email: j.m.h.thomas(-)dl.ac.uk STFC Daresbury Lab, tel: +44-1925-603849 Warrington, fax: +44-1925-603634 WA4 4AD, UK. http: http://www.cse.scitech.ac.uk =================================================================== From owner-chemistry@ccl.net Mon Sep 17 09:10:00 2007 From: "Julien Lefeuvre j.lefeuvre%x%iecb.u-bordeaux.fr" To: CCL Subject: CCL: Smiles -> Isis draw Message-Id: <-35173-070917053130-8647-WyOFqSlETFGklbeeX88Ubw!^!server.ccl.net> X-Original-From: Julien Lefeuvre Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15 Date: Mon, 17 Sep 2007 10:58:29 +0200 MIME-Version: 1.0 Sent to CCL by: Julien Lefeuvre [j.lefeuvre(!)iecb.u-bordeaux.fr] Jerome Kieffer jerome.Kieffer . terre-adelie.org wrote: > I am wondering if any of yours has a piece of software to convert a > molecule represented as it's SMILES string into a ".skc" isis draw > file. The best would be an open-source code so that I could re-use it > but if it is «just» free, it is OK for me. I know 3 open source software able to convert SMILES code to flat 2D representation: bkckem xdrawchem and of course openbabel I don't know if either support the Isis draw file format, but Isis should be able to import CML files. HIH cheers Julien Lefeuvre -- Computers are useless; they can only give you answers! -Picasso From owner-chemistry@ccl.net Mon Sep 17 09:54:01 2007 From: "Kalyan chaitanya kalyanpulipaka^gmail.com" To: CCL Subject: CCL: query.... Message-Id: <-35174-070917094851-5636-9p+OCi4bxVM16jdexBAppA() server.ccl.net> X-Original-From: "Kalyan chaitanya" Content-Type: multipart/alternative; boundary="----=_Part_7521_686153.1190036924545" Date: Mon, 17 Sep 2007 19:18:44 +0530 MIME-Version: 1.0 Sent to CCL by: "Kalyan chaitanya" [kalyanpulipaka++gmail.com] ------=_Part_7521_686153.1190036924545 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all, Iam using AUTODOCK for docking a receptor with its natural ligand at its binding site, iam able to dock and even able to analyze the results and split the dlg file, but to my surprise, it shows very high docked energy at its binding site, where as when iam putting the grid for whole molecule (as in blind docking ) it shows docked energy approximately -9 but it is binding some other place not at its binding site. To confirm the results i used diferent softwares to dock the same receptor with its natural ligand they are also showing me the same results as AUTODOCK, but i have experimental data saying that the natural ligand binds at its binding site. what could be wrong, can any one help me in this regard. Thankyou in advance, Kalyan.P ------=_Part_7521_686153.1190036924545 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline

Dear all,

Iam using AUTODOCK for docking a receptor with its natural ligand at its binding site, iam able to dock and even able to analyze the results and split the dlg file, but to my surprise, it shows very high docked energy at its binding site, where as when iam putting the grid for whole molecule (as in blind docking ) it shows docked energy approximately -9 but it is binding some other place not at its binding site.

To confirm the results i used diferent softwares to dock the same receptor with its natural ligand they are also showing me the same results as AUTODOCK, but i have experimental data saying that the natural ligand binds at its binding site. what could be wrong, can any one help me in this regard.

Thankyou in advance,

Kalyan.P

------=_Part_7521_686153.1190036924545-- From owner-chemistry@ccl.net Mon Sep 17 10:28:01 2007 From: "Forlani Roberto roberto.forlani*o*nikemresearch.com" To: CCL Subject: CCL: Smiles -> Isis draw Message-Id: <-35175-070917100342-14057-/g4lbIUpJUNpwVImvZRD1Q+*+server.ccl.net> X-Original-From: "Forlani Roberto" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 17 Sep 2007 15:31:14 +0200 MIME-Version: 1.0 Sent to CCL by: "Forlani Roberto" [roberto.forlani,+,nikemresearch.com] =20 > -----Original Message----- > From: owner-chemistry===ccl.net [mailto:owner-chemistry===ccl.net]=20 > Sent: 16 September 2007 21:55 > To: Forlani Roberto > Subject: CCL: Smiles -> Isis draw >=20 >=20 > Sent to CCL by: Jerome Kieffer=20 > [jerome.Kieffer^terre-adelie.org] Dear CCLers, >=20 > I am wondering if any of yours has a piece of software to=20 > convert a molecule represented as it's SMILES string into a=20 > ".skc" isis draw file. The best would be an open-source code=20 > so that I could re-use it but if it is =ABjust=BB free, it is OK for = me. >=20 > Best regards. > -- > J=E9r=F4me KIEFFER : http://www.terre-adelie.org =C0 v=E9lo, prendre=20 > une rue =E0 contre-sens est moins dangeureux que prendre un=20 > boulevard dans le sens l=E9gal. =C0 qui la faute ? Jerome, to my knowledge no free/open source Isis/Draw sketches writer are = available (MDL ConSystant is the commercial alternative). You can think to convert (and split) multi smiles to mol by means of = openbabel. Isis/Draw can open obtained mol files. Hope this helps. Regards, Roberto From owner-chemistry@ccl.net Mon Sep 17 12:27:00 2007 From: "Wendy A Warr wendy|,|warr.com" To: CCL Subject: CCL: Scholarship announcement Message-Id: <-35176-070917122056-28392-8KEBgeDn31JA4BKZwj8G0A]|[server.ccl.net> X-Original-From: "Wendy A Warr" Date: Mon, 17 Sep 2007 12:20:51 -0400 Sent to CCL by: "Wendy A Warr" [wendy^warr.com] Posted on behalf of Guenter Grethe ggrethe~!~comcast.net CINF Scholarship for Scientific Excellence Sponsored by FIZ CHEMIE Berlin The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by FIZ CHEMIE Berlin is designed to reward graduate and post-graduate students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Three scholarships valued at 1,000 were given out at the 2007 Fall ACS National Meeting in Boston. The winners showed their award-winning posters at the Sci-Mix session of the same meeting. They were presented with their awards at the divisional luncheon. The names of the recipients and the titles of their posters are: Thuan Thi Hoang Huynh Buu, University of Applied Science, 4232 Hagenberg, Austria, A scoring function to rank pharmacophoric alignments and its application to H-1 antagonists; Dazhi Jiao, School of Informatics, Indiana University at Bloomington, Bloomington, IN 47408, Using a chatbot to access chemical information; Raghava Chaitanya Kasara, Chemistry Department, Clarkson University, Potsdam, NY 13699, Pharmacodynamic modeling of C2 symmetric HIV-1 protease inhibitors. Five scholarships valued at 1,000 each funded by Elsevier MDL will be awarded at the Spring ACS National Meeting in New Orleans, April 6 -10, 2008. In order to apply for these scholarships please see the relevant announcement on the CINF website (http://www.acscinf.org/) under Recent Announcements. Guenter Grethe, CINF Awards Chair From owner-chemistry@ccl.net Mon Sep 17 13:02:00 2007 From: "Wendy A Warr wendy(a)warr.com" To: CCL Subject: CCL: Scholarship applications sought Message-Id: <-35177-070917122322-28607-AreCK9YjsV+Rt9KGX3AzSg : server.ccl.net> X-Original-From: "Wendy A Warr" Date: Mon, 17 Sep 2007 12:23:18 -0400 Sent to CCL by: "Wendy A Warr" [wendy[#]warr.com] Posted on behalf of Guenter Grethe ggrethe]*[comcast.net CINF Scholarship for Scientific Excellence Sponsored by Elsevier MDL The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by Elsevier MDL is designed to reward graduate and postdoctoral students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Up to five scholarships valued at 1,000 each will be presented at the 235th ACS National Meeting in New Orleans, April 6 10, 2008. Applicants must be enrolled at a certified college or university, and they will present a poster during the Sci-Mix session at the National Meeting. Abstracts for the poster must be submitted electronically through OASYS. To apply, please inform the Chair of the selection committee, Guenter Grethe at ggrethe]*[comcast.net, that you are applying for a scholarship. Submit your abstract at http://oasys.acs.org/acs/235nm/cinf/papers/index.cgi by clicking on Sci-Mix Posters. To enter your abstract, just follow the instructions. The deadline for submitting an abstract to OASYS is November 4, 2007. Additionally, please send a 2,000-word abstract describing the work to be presented in electronic form to the Chair of the selection committee by January 15, 2008. Any questions related to applying for one of the scholarships should be directed to the same e-mail address. Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced at the meeting. The contents shall reflect upon the students work and describe research in the field of cheminformatics and related sciences. Winning posters will be marked Winner of Elsevier MDL-CINF Scholarship for Scientific Excellence at the poster session. Guenter Grethe From owner-chemistry@ccl.net Mon Sep 17 13:36:01 2007 From: "Wendy A Warr wendy]-[warr.com" To: CCL Subject: CCL: Call for nominations for Award Message-Id: <-35178-070917122536-28755-r1xM0PObESvsYnftDmXmiw]=[server.ccl.net> X-Original-From: "Wendy A Warr" Date: Mon, 17 Sep 2007 12:25:32 -0400 Sent to CCL by: "Wendy A Warr" [wendy^warr.com] Posted on behalf of Guenter Grethe ggrethe * comcast.net 2009 Herman Skolnik Award Call for Nominations The ACS Division of Chemical Information established this Award to recognize outstanding contributions to and achievements in the theory and practice of chemical information science. The Award is named in honor of the first recipient, Herman Skolnik. By this Award, the Division of Chemical Information is committed to encouraging the continuing preparation, dissemination and advancement of chemical information science and related disciplines through individual and team efforts. Examples of such advancement include, but are not limited to, the following: Design of new and unique computerized information systems; Preparation and dissemination of chemical information; Editorial innovations; Design of new indexing, classification, and notation systems; Chemical nomenclature; Structure-activity relationships; and Numerical data correlation and evaluation. Advancement of knowledge in the field The Award consists of a 3000 honorarium and a plaque. The recipient is expected to give an address at the time of the Award presentation. In recent years, the Award Symposium has been organized by the recipient. Nominations for the Herman Skolnik Award should describe the nominee's contributions to the field of chemical information and should include supportive materials such as a biographical sketch and a list of publications and presentations. Three seconding letters are also required. Nominations and supporting material should be sent by email to me (ggrethe * comcast.net). Paper submissions are no longer acceptable. The deadline for nominations for the 2009 Herman Skolnik Award is June 1, 2008. Guenter Grethe, CINF Awards Chair From owner-chemistry@ccl.net Mon Sep 17 14:12:01 2007 From: "Elaine Meng meng(a)cgl.ucsf.edu" To: CCL Subject: CCL:G: Orbitals/cube/Mac OS X Message-Id: <-35179-070917125618-19929-Yg9fpY1MJl5eta30SqNE9g^^server.ccl.net> X-Original-From: "Elaine Meng" Date: Mon, 17 Sep 2007 12:56:12 -0400 Sent to CCL by: "Elaine Meng" [meng*|*cgl.ucsf.edu] Hi Frank, Chimera is another possibility for viewing orbitals (Gaussian cube grid or gOpenMol format) along with molecules on Mac OS X. Chimera home page: http://www.cgl.ucsf.edu/chimera/index.html Download is free for academic, nonprofit, or personal use: http://www.cgl.ucsf.edu/chimera/download.html The interface for viewing grid data (Volume Viewer) has many features and allows showing data as isosurfaces or semitransparent volumes: http://www.cgl.ucsf.edu/chimera/1.2422/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html Best, Elaine ----- Elaine C. Meng, Ph.D. meng%a%cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From owner-chemistry@ccl.net Mon Sep 17 14:50:01 2007 From: "pragya chohan pragyachohan],[hotmail.com" To: CCL Subject: CCL:G: gaussian Message-Id: <-35180-070917130242-23203-nR6ysY7kKZ8RBh7hudaVzw\a/server.ccl.net> X-Original-From: "pragya chohan" Date: Mon, 17 Sep 2007 13:02:39 -0400 Sent to CCL by: "pragya chohan" [pragyachohan!^!hotmail.com] hi.. i m getting the following error... i guess it is because of lack of memory.... is it really so.... pls help Out-of-memory error in routine After all major allocation (IEnd= 1229340 MxCore= 969022) Use %mem=7MW to provide the minimum amount of memory required to complete this step. Error termination via Lnk1e in /nepdisk11/g03/l502.exe at Mon Sep 17 20:59:14 2007. From owner-chemistry@ccl.net Mon Sep 17 15:22:00 2007 From: "Jerome Kieffer jerome.Kieffer]|[terre-adelie.org" To: CCL Subject: CCL: Smiles -> Isis draw Message-Id: <-35181-070917133234-11460-TSDWckBdIQD+18WJ0711Mw#%#server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Mon, 17 Sep 2007 19:32:28 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer{:}terre-adelie.org] On Mon, 17 Sep 2007 10:58:29 +0200 "Julien Lefeuvre j.lefeuvre%x%iecb.u-bordeaux.fr" wrote: > I know 3 open source software able to convert SMILES code to flat 2D > representation: > bkckem > xdrawchem > and of course openbabel I know babel and openbabel for half a dozen year now and I wonder how to convert a smiles into a 2D or a 3D because I got all coordinate to zero. benzene.smi=3D"c1ccccc1" babel benzene.smi benzene.xyz cat benzene.xyz 6 benzene.smi C 0.00000 0.00000 0.00000 C 0.00000 0.00000 0.00000 C 0.00000 0.00000 0.00000 C 0.00000 0.00000 0.00000 C 0.00000 0.00000 0.00000 C 0.00000 0.00000 0.00000 Do you have a trick to have =ABnon-zero=BB position ? Thanks. --=20 J=E9r=F4me KIEFFER : http://www.terre-adelie.org =C0 v=E9lo, prendre une rue =E0 contre-sens est moins dangeureux que prendre un boulevard dans le sens l=E9gal. =C0 qui la faute ? From owner-chemistry@ccl.net Mon Sep 17 15:59:01 2007 From: "Jerome Kieffer jerome.Kieffer===terre-adelie.org" To: CCL Subject: CCL: Fw: Re: CCL: Smiles -> Isis draw Message-Id: <-35182-070917154744-12504-bc2gnNhguOl/f2xFqn4yQw|server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Mon, 17 Sep 2007 21:47:38 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer/a\terre-adelie.org] On Mon, 17 Sep 2007 10:58:29 +0200 "Julien Lefeuvre j.lefeuvre%x%iecb.u-bordeaux.fr" wrote: > I know 3 open source software able to convert SMILES code to flat 2D > representation: > bkckem > xdrawchem > and of course openbabel I know babel and openbabel for half a dozen year now and I wonder how to convert a smiles into a 2D or a 3D because I got all coordinate to zero. benzene.smi=3D"c1ccccc1" babel benzene.smi benzene.xyz cat benzene.xyz 6 benzene.smi C 0.00000 0.00000 0.00000 C 0.00000 0.00000 0.00000 C 0.00000 0.00000 0.00000 C 0.00000 0.00000 0.00000 C 0.00000 0.00000 0.00000 C 0.00000 0.00000 0.00000 Do you have a trick to have "non-zero" positions ? Thanks. --=20 J=E9r=F4me KIEFFER : http://www.terre-adelie.org From owner-chemistry@ccl.net Mon Sep 17 16:32:01 2007 From: "Ivanciuc, Ovidiu I. oiivanci _ utmb.edu" To: CCL Subject: CCL: Smiles -> 2D & 3D Message-Id: <-35183-070917160949-29511-y/n2EmdaxcXiz6XZcvIzow!A!server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 17 Sep 2007 15:05:16 -0500 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci++utmb.edu] >>I wonder how to convert a smiles into a 2D or a 3D because >> I got all coordinate to zero. for SMILES -> 2D: GIF/PNG-Creator http://cactus.nci.nih.gov/services/gifcreator/ for SMILES -> 2D &3D: SDF, PDB, MOL http://cactus.nci.nih.gov/services/translate/ O. From owner-chemistry@ccl.net Mon Sep 17 17:07:01 2007 From: "Igor Filippov Contr igorf[-]helix.nih.gov" To: CCL Subject: CCL: Smiles -> Isis draw Message-Id: <-35184-070917164740-24824-rrywwblmWNfTIHntHQ+4RQ|server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=Windows-1251 Date: Mon, 17 Sep 2007 16:47:25 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf===helix.nih.gov] There was announcement about smi23d quite recently on CCL. http://www.chembiogrid.org/cheminfo/threed/d3 Igor On Mon, 2007-09-17 at 19:32 +0200, Jerome Kieffer jerome.Kieffer]|[terre-adelie.org wrote: > Sent to CCL by: Jerome Kieffer [jerome.Kieffer{:}terre-adelie.org] > On Mon, 17 Sep 2007 10:58:29 +0200 > "Julien Lefeuvre j.lefeuvre%x%iecb.u-bordeaux.fr" > wrote: > > > I know 3 open source software able to convert SMILES code to flat 2D > > representation: > > bkckem > > xdrawchem > > and of course openbabel > > I know babel and openbabel for half a dozen year now and I wonder how > to convert a smiles into a 2D or a 3D because I got all coordinate to > zero. > > benzene.smi="c1ccccc1" > > babel benzene.smi benzene.xyz > cat benzene.xyz > > 6 > benzene.smi > C 0.00000 0.00000 0.00000 > C 0.00000 0.00000 0.00000 > C 0.00000 0.00000 0.00000 > C 0.00000 0.00000 0.00000 > C 0.00000 0.00000 0.00000 > C 0.00000 0.00000 0.00000 > > Do you have a trick to have «non-zero» position ? > Thanks. From owner-chemistry@ccl.net Mon Sep 17 20:49:00 2007 From: "richard apodaca rich_apodaca]*[yahoo.com" To: CCL Subject: CCL: Fw: Re: CCL: Smiles -> Isis draw Message-Id: <-35185-070917175248-3575-c6ALrj/CA4OxMQHqHT4q1A_-_server.ccl.net> X-Original-From: richard apodaca Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 17 Sep 2007 13:52:39 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: richard apodaca [rich_apodaca]_[yahoo.com] Well, if you're willing to try Ruby (and/or Java), it's quite easy to get 2D coordinates for arbitrary SMILES strings: http://depth-first.com/articles/2006/12/04/anatomy-of-a-cheminformatics-web-application-ajaxifying-depict This approach takes advantage of the excellent support the Chemistry Development Kit (CDK) has for Stucture Diagram Generation (SDG). If InChIs are your thing, using Open Babel and CDK together with Ruby gives a simple solution to the problem (and even full-color images if you'd like): http://depth-first.com/articles/2007/09/06/from-inchi-to-image-with-ruby-open-babel-and-ruby-cdk Both approaches use 100% open source software. The CDK is even LGPL. --- "Jerome Kieffer jerome.Kieffer===terre-adelie.org" wrote: > > Sent to CCL by: Jerome Kieffer > [jerome.Kieffer/a\terre-adelie.org] > > > > On Mon, 17 Sep 2007 10:58:29 +0200 > "Julien Lefeuvre j.lefeuvre%x%iecb.u-bordeaux.fr" > wrote: > > > I know 3 open source software able to convert > SMILES code to flat 2D > > representation: > > bkckem > > xdrawchem > > and of course openbabel > > I know babel and openbabel for half a dozen year now > and I wonder how > to convert a smiles into a 2D or a 3D because I got > all coordinate to > zero. > > benzene.smi="c1ccccc1" > > babel benzene.smi benzene.xyz > cat benzene.xyz > > 6 > benzene.smi > C 0.00000 0.00000 0.00000 > C 0.00000 0.00000 0.00000 > C 0.00000 0.00000 0.00000 > C 0.00000 0.00000 0.00000 > C 0.00000 0.00000 0.00000 > C 0.00000 0.00000 0.00000 > > Do you have a trick to have "non-zero" positions ? > Thanks. > -- > Jérôme KIEFFER : http://www.terre-adelie.org > > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the {=} > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST{=}ccl.net > or use> > Before posting, check wait time at: > http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: > ccl, Password: search) > > If your mail bounces from CCL with 5.7.1 error, > check:> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/> > > > ___________________________________ Richard L. Apodaca http://depth-first.com Blog http://metamolecular.com Company From owner-chemistry@ccl.net Mon Sep 17 21:24:01 2007 From: "Julie H Hwang jhwang5:_:mail.rochester.edu" To: CCL Subject: CCL:G: GAUSSIAN-basis sets Message-Id: <-35186-070917210652-30241-6EjN11qAwBmu2aob/t292A-,-server.ccl.net> X-Original-From: "Julie H Hwang" Date: Mon, 17 Sep 2007 21:06:48 -0400 Sent to CCL by: "Julie H Hwang" [jhwang5=-=mail.rochester.edu] Dear all, Hi I have a question on choosing basis set(s). I want to calculate Raman spectra peaks for ferrocene and I was wondering if I can choose different basis sets for non-metals (C and H) and metal (Fe). I tried to look up the Gaussian manual, but they didn't specify the availability of such option. Thank you for your time!