From owner-chemistry@ccl.net Wed Jan 11 08:27:00 2006 From: "Jinsong Zhao jszhao%mail.hzau.edu.cn" To: CCL Subject: CCL: quantum simulation for oxide surface Message-Id: <-30454-060111082537-5197-Fc3vTtWq4drNeatmxYP89w|-|server.ccl.net> X-Original-From: "Jinsong Zhao" Sent to CCL by: "Jinsong Zhao" [jszhao..mail.hzau.edu.cn] Dear all, I am wondering it's possible to simulate the chemicals interaction that occurred at metal oxide surfaces in aqueous environment using quantum computation. And some recommended references would be really appreciated. Thanks in advance! Best wishes, Jinsong Zhao == Jinsong Zhao, Dr. College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, P. R. China E-mail: jszhao++mail.hzau.edu.cn From owner-chemistry@ccl.net Wed Jan 11 12:48:00 2006 From: "Leif Olson leif.olson~~kodak.com" To: CCL Subject: CCL: Simple molecular graphics Message-Id: <-30455-060111124543-26521-sLwFJNyxHuUB6bFbuRLrqw*server.ccl.net> X-Original-From: "Leif Olson" Sent to CCL by: "Leif Olson" [leif.olson,,kodak.com] Hi CCL people, I know this is similar to previous questions that have been sent to the list in the past. But I am going to ask it anyway...I keep searching for a program that will make simple publication quality molecular graphics pictures (usually black-and-white), but with a couple of added features, and runs on Windows or Linux. Vast numbers of molecular graphics programs are advertised for their capability to make "publication quality" images. But what this always seems to refer to is the ability to create stunning color pictures complete with shadows, fog effects, dramatic backgrounds, etc., perhaps rendered with the help of POV-Ray. Nice, but not what I usually need for figures to put into journal articles or technical reports. I usually just want ball-and-stick, black-and-white (or a simple color scheme to highlight heteroatoms), maybe some cross-hatching to suggest depth, and some labeling capability, with the end result a high-resolution image or vector output. An example of a program that comes pretty close to what I would like is XChemEdit, where I can read in a structure, and quickly rotate/translate it to a desired orientation. Then, with a few mouse clicks I can remove undesired bonds, make dashed bonds (e.g. for hydrogen bonds or transition states), label bond distances/angles/dihedrals, resize and move labels, etc. This only takes a minute or two, unfortunately the resulting images are not, in my opinion, good enough for external publication. They are nicely labeled and clear, but low-resolution. As an alternative, I have tried Schakal99, which can make excellent publication-quality b/w molecular graphics, and it seems that one has extensive control over the final image. But I find it difficult to use even after studying the manual and going through quite a few examples, and I am not sure that certain things like labeling bond angles can even be done. I have also looked at XBS, Molden, ORTEP, and WebLab Viewer, but they aren't quite what I am looking for either. We don't own Cache, Chem3D, or Gaussview, so I haven't tried them...what about those or other software? Is it best to just put in the time to really learn Schakal usage? Would you agree that fancy photorealistic "publication quality" graphics are often discouraged by journal editors anyway? Thanks! Leif Olson Eastman Kodak Research Laboratories From owner-chemistry@ccl.net Wed Jan 11 15:04:00 2006 From: "David van der Spoel spoel|,|xray.bmc.uu.se" To: CCL Subject: CCL: Simple molecular graphics Message-Id: <-30456-060111141001-24919-lSavQdbgNqz9rAZl5pJVWQ-.-server.ccl.net> X-Original-From: David van der Spoel Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 11 Jan 2006 19:27:53 +0100 MIME-Version: 1.0 Sent to CCL by: David van der Spoel [spoel*xray.bmc.uu.se] Leif Olson leif.olson~~kodak.com wrote: > Sent to CCL by: "Leif Olson" [leif.olson,,kodak.com] > Hi CCL people, > > I know this is similar to previous questions that have been sent to the list in the past. But I am going to ask it anyway...I keep searching for a program that will make simple publication quality molecular graphics pictures (usually black-and-white), but with a couple of added features, and runs on Windows or Linux. > http://pymol.sf.net > Vast numbers of molecular graphics programs are advertised for their capability to make "publication quality" images. But what this always seems to refer to is the ability to create stunning color pictures complete with shadows, fog effects, dramatic backgrounds, etc., perhaps rendered with the help of POV-Ray. Nice, but not what I usually need for figures to put into journal articles or technical reports. I usually just want ball-and-stick, black-and-white (or a simple color scheme to highlight heteroatoms), maybe some cross-hatching to suggest depth, and some labeling capability, with the end result a high-resolution image or vector output. > > An example of a program that comes pretty close to what I would like is XChemEdit, where I can read in a structure, and quickly rotate/translate it to a desired orientation. Then, with a few mouse clicks I can remove undesired bonds, make dashed bonds (e.g. for hydrogen bonds or transition states), label bond distances/angles/dihedrals, resize and move labels, etc. This only takes a minute or two, unfortunately the resulting images are not, in my opinion, good enough for external publication. They are nicely labeled and clear, but low-resolution. > > As an alternative, I have tried Schakal99, which can make excellent publication-quality b/w molecular graphics, and it seems that one has extensive control over the final image. But I find it difficult to use even after studying the manual and going through quite a few examples, and I am not sure that certain things like labeling bond angles can even be done. > > I have also looked at XBS, Molden, ORTEP, and WebLab Viewer, but they aren't quite what I am looking for either. We don't own Cache, Chem3D, or Gaussview, so I haven't tried them...what about those or other software? Is it best to just put in the time to really learn Schakal usage? Would you agree that fancy photorealistic "publication quality" graphics are often discouraged by journal editors anyway? > > Thanks! > > Leif Olson > Eastman Kodak Research Laboratories> > -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel]|[xray.bmc.uu.se spoel]|[gromacs.org http://xray.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-chemistry@ccl.net Wed Jan 11 15:39:01 2006 From: "Wayne Steinmetz WES04747**pomona.edu" To: CCL Subject: CCL: Simple molecular graphics Message-Id: <-30457-060111144146-28641-oKVz50rHkQRry6MDf1ml2g_+_server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 11 Jan 2006 10:41:49 -0800 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747 ~~ pomona.edu] I use Tripos' SYBYL to generate pictures of structures. Wavefunction's Spartan also does a nice job. The license for Spartan is reasonably priced. Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-707-7726 Email: wsteinmetz(_)pomona.edu WWW: pages.pomona.edu/~wsteinmetz -----Original Message----- > From: owner-chemistry(_)ccl.net [mailto:owner-chemistry(_)ccl.net] Sent: Wednesday, January 11, 2006 10:08 AM To: Wayne Steinmetz Subject: CCL: Simple molecular graphics Sent to CCL by: "Leif Olson" [leif.olson,,kodak.com] Hi CCL people, I know this is similar to previous questions that have been sent to the list in the past. But I am going to ask it anyway...I keep searching for a program that will make simple publication quality molecular graphics pictures (usually black-and-white), but with a couple of added features, and runs on Windows or Linux. Vast numbers of molecular graphics programs are advertised for their capability to make "publication quality" images. But what this always seems to refer to is the ability to create stunning color pictures complete with shadows, fog effects, dramatic backgrounds, etc., perhaps rendered with the help of POV-Ray. Nice, but not what I usually need for figures to put into journal articles or technical reports. I usually just want ball-and-stick, black-and-white (or a simple color scheme to highlight heteroatoms), maybe some cross-hatching to suggest depth, and some labeling capability, with the end result a high-resolution image or vector output. An example of a program that comes pretty close to what I would like is XChemEdit, where I can read in a structure, and quickly rotate/translate it to a desired orientation. Then, with a few mouse clicks I can remove undesired bonds, make dashed bonds (e.g. for hydrogen bonds or transition states), label bond distances/angles/dihedrals, resize and move labels, etc. This only takes a minute or two, unfortunately the resulting images are not, in my opinion, good enough for external publication. They are nicely labeled and clear, but low-resolution. As an alternative, I have tried Schakal99, which can make excellent publication-quality b/w molecular graphics, and it seems that one has extensive control over the final image. But I find it difficult to use even after studying the manual and going through quite a few examples, and I am not sure that certain things like labeling bond angles can even be done. I have also looked at XBS, Molden, ORTEP, and WebLab Viewer, but they aren't quite what I am looking for either. We don't own Cache, Chem3D, or Gaussview, so I haven't tried them...what about those or other software? Is it best to just put in the time to really learn Schakal usage? Would you agree that fancy photorealistic "publication quality" graphics are often discouraged by journal editors anyway? Thanks! Leif Olson Eastman Kodak Research Laboratorieshttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software. From owner-chemistry@ccl.net Wed Jan 11 16:14:01 2006 From: "Warren DeLano warren#delsci.com" To: CCL Subject: CCL: Simple molecular graphics Message-Id: <-30458-060111153556-26700-QGHIdpNUSNZDeeFZtSXcUw#server.ccl.net> X-Original-From: "Warren DeLano" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 11 Jan 2006 11:50:40 -0800 MIME-Version: 1.0 Sent to CCL by: "Warren DeLano" [warren(a)delsci.com] Leif, PyMOL can now do black & white nicely, as well as photorealistic color on black, white, or transparent backgrounds. It can be used for everything from electron density, ball & stick, and cartoon, all the way way up to megadalton EM tomography surface representations. Some examples at: http://www.pymolwiki.org/index.php/Ray Latest builds d/l at http://delsci.com/beta Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren|a|delsci.com > -----Original Message----- > From: owner-chemistry|a|ccl.net [mailto:owner-chemistry|a|ccl.net] > Sent: Wednesday, January 11, 2006 10:46 AM > To: Warren DeLano > Subject: CCL: Simple molecular graphics > > Sent to CCL by: "Leif Olson" [leif.olson,,kodak.com] Hi CCL people, > > I know this is similar to previous questions that have been > sent to the list in the past. But I am going to ask it > anyway...I keep searching for a program that will make simple > publication quality molecular graphics pictures (usually > black-and-white), but with a couple of added features, and > runs on Windows or Linux. > > Vast numbers of molecular graphics programs are advertised > for their capability to make "publication quality" images. > But what this always seems to refer to is the ability to > create stunning color pictures complete with shadows, fog > effects, dramatic backgrounds, etc., perhaps rendered with > the help of POV-Ray. Nice, but not what I usually need for > figures to put into journal articles or technical reports. I > usually just want ball-and-stick, black-and-white (or a > simple color scheme to highlight heteroatoms), maybe some > cross-hatching to suggest depth, and some labeling > capability, with the end result a high-resolution image or > vector output. > > An example of a program that comes pretty close to what I > would like is XChemEdit, where I can read in a structure, and > quickly rotate/translate it to a desired orientation. Then, > with a few mouse clicks I can remove undesired bonds, make > dashed bonds (e.g. for hydrogen bonds or transition states), > label bond distances/angles/dihedrals, resize and move > labels, etc. This only takes a minute or two, unfortunately > the resulting images are not, in my opinion, good enough for > external publication. They are nicely labeled and clear, but > low-resolution. > > As an alternative, I have tried Schakal99, which can make > excellent publication-quality b/w molecular graphics, and it > seems that one has extensive control over the final image. > But I find it difficult to use even after studying the manual > and going through quite a few examples, and I am not sure > that certain things like labeling bond angles can even be done. > > I have also looked at XBS, Molden, ORTEP, and WebLab Viewer, > but they aren't quite what I am looking for either. We don't > own Cache, Chem3D, or Gaussview, so I haven't tried > them...what about those or other software? Is it best to > just put in the time to really learn Schakal usage? Would > you agree that fancy photorealistic "publication quality" > graphics are often discouraged by journal editors anyway? > > Thanks! > > Leif Olson > Eastman Kodak Research Laboratories > > > > -= 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 |a| sign. You can also look up the X-Original-From: line > in the mail header.> > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > > > From owner-chemistry@ccl.net Wed Jan 11 16:48:01 2006 From: "IEJMD iejmd|yahoo.com" To: CCL Subject: CCL: Invitation to CoEPrA 2006 - Data Modeling Competition Message-Id: <-30459-060111160505-11732-CYuXm2lI+pPtMhBydKEtYg[*]server.ccl.net> X-Original-From: IEJMD Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 11 Jan 2006 12:04:56 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: IEJMD [iejmd!A!yahoo.com] CoEPrA 2006 - Comparative Evaluation of Prediction Algorithms http://www.coepra.org/ Dear Colleague, You are cordially invited to participate in the CoEPrA 2006 Competition, which will start on April 17, 2006. CoEPrA (Comparative Evaluation of Prediction Algorithms) is a modeling competition organized to provide an objective testing for various classification and regression algorithms via the process of blind prediction. The problems proposed in the CoEPrA experiment are selected from cheminformatics, drug design, QSAR, bioinformatics, computational biology, medicine, toxicology, microarray gene expression data, and proteomics. The goal of the CoEPrA competition is to advance the algorithms and software for modeling chemical, biological, and medical data, with special emphasis on the prediction of physico-chemical properties and biological activities from molecular descriptors derived from the chemical structure. In addition, CoEPrA will provide a reference database of modeling datasets that can be used to validate and compare new classification and regression algorithms. In each CoEPrA task the participants receive a calibration dataset and a prediction dataset. The model (classification or regression) derived from the calibration dataset is used to predict the dependent variable of the prediction dataset. These predictions must be deposited before the deadline of each task. The Organizers and Evaluators for each CoEPrA task will evaluate all predictions and will anounce the ranking of the participants. For details, see http://www.coepra.org/ Best regards, Ovidiu Ivanciuc ###################################### Ovidiu Ivanciuc Sealy Center for Structural Biology, Department of Biochemistry and Molecular Biology University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0857 USA Email: oiivanci%%utmb.edu Email: iejmd%%yahoo.com IEJMD: http://www.biochempress.com __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Wed Jan 11 17:24:01 2006 From: "JAMES VIVIAN jamestvivian(-)msn.com" To: CCL Subject: CCL: Simple molecular graphics Message-Id: <-30460-060111161834-16128-uvQzj3GqZ5FEXaaNlnanjA---server.ccl.net> X-Original-From: "JAMES VIVIAN" Content-Type: text/plain; format=flowed Date: Wed, 11 Jan 2006 16:18:24 -0500 Mime-Version: 1.0 Sent to CCL by: "JAMES VIVIAN" [jamestvivian{=}msn.com] Maestro (from Schrodinger) provides a very robust graphics capability, and can produce 600dpi publication quality graphics. It is available as a standalone module for free to academic groups, as announced recently on this List. Available by download from www.schrodinger.com. >From: "Wayne Steinmetz WES04747**pomona.edu" >Reply-To: "CCL Subscribers" >To: "Vivian, James T " >Subject: CCL: Simple molecular graphics >Date: Wed, 11 Jan 2006 15:52:28 -0500 > >Sent to CCL by: "Wayne Steinmetz" [WES04747 ~~ pomona.edu] >I use Tripos' SYBYL to generate pictures of structures. Wavefunction's >Spartan also does a nice job. The license for Spartan is reasonably >priced. > >Wayne E. Steinmetz >Carnegie Professor of Chemistry >Woodbadge Course Director >Chemistry Department >Pomona College >645 North College Avenue >Claremont, California 91711-6338 >USA >phone: 1-909-621-8447 >FAX: 1-909-707-7726 >Email: wsteinmetz[a]pomona.edu >WWW: pages.pomona.edu/~wsteinmetz > > >-----Original Message----- > > From: owner-chemistry[a]ccl.net [mailto:owner-chemistry[a]ccl.net] >Sent: Wednesday, January 11, 2006 10:08 AM >To: Wayne Steinmetz >Subject: CCL: Simple molecular graphics > >Sent to CCL by: "Leif Olson" [leif.olson,,kodak.com] >Hi CCL people, > >I know this is similar to previous questions that have been sent to the >list in the past. But I am going to ask it anyway...I keep searching >for a program that will make simple publication quality molecular >graphics pictures (usually black-and-white), but with a couple of added >features, and runs on Windows or Linux. > >Vast numbers of molecular graphics programs are advertised for their >capability to make "publication quality" images. But what this always >seems to refer to is the ability to create stunning color pictures >complete with shadows, fog effects, dramatic backgrounds, etc., perhaps >rendered with the help of POV-Ray. Nice, but not what I usually need >for figures to put into journal articles or technical reports. I >usually just want ball-and-stick, black-and-white (or a simple color >scheme to highlight heteroatoms), maybe some cross-hatching to suggest >depth, and some labeling capability, with the end result a >high-resolution image or vector output. > >An example of a program that comes pretty close to what I would like is >XChemEdit, where I can read in a structure, and quickly rotate/translate >it to a desired orientation. Then, with a few mouse clicks I can remove >undesired bonds, make dashed bonds (e.g. for hydrogen bonds or >transition states), label bond distances/angles/dihedrals, resize and >move labels, etc. This only takes a minute or two, unfortunately the >resulting images are not, in my opinion, good enough for external >publication. They are nicely labeled and clear, but low-resolution. > >As an alternative, I have tried Schakal99, which can make excellent >publication-quality b/w molecular graphics, and it seems that one has >extensive control over the final image. But I find it difficult to use >even after studying the manual and going through quite a few examples, >and I am not sure that certain things like labeling bond angles can even >be done. > >I have also looked at XBS, Molden, ORTEP, and WebLab Viewer, but they >aren't quite what I am looking for either. We don't own Cache, Chem3D, >or Gaussview, so I haven't tried them...what about those or other >software? Is it best to just put in the time to really learn Schakal >usage? Would you agree that fancy photorealistic "publication quality" >graphics are often discouraged by journal editors anyway? > >Thanks! > >Leif Olson >Eastman Kodak Research >Laboratorieshttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------------------------------------------------------------- >This message has been scanned by Postini anti-virus software.> > > From owner-chemistry@ccl.net Wed Jan 11 17:59:01 2006 From: "Rydberg, Patrik - Patrik.Rydberg*|*teokem.lu.se" To: CCL Subject: CCL: Simple molecular graphics Message-Id: <-30461-060111165909-12343-sjTkfeSQkqNuutuV37Ovgg===server.ccl.net> X-Original-From: "Rydberg, Patrik -" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 11 Jan 2006 22:18:06 +0100 MIME-Version: 1.0 Sent to CCL by: "Rydberg, Patrik -" [Patrik.Rydberg.~!~.teokem.lu.se] The easiest solution I've found is using Xdrawchem to build my structures and then save them as SVG-format. Open the SVG file in Inkscape where you can add and edit anything you need and also export high quality image files. http://xdrawchem.sourceforge.net/ http://www.inkscape.org Patrik Rydberg Theoretical chemistry, Lund University Leif Olson leif.olson~~kodak.com wrote: >Sent to CCL by: "Leif Olson" [leif.olson,,kodak.com] >Hi CCL people, > >I know this is similar to previous questions that have been sent to the list in the past. But I am going to ask it anyway...I keep searching for a program that will make simple publication quality molecular graphics pictures (usually black-and-white), but with a couple of added features, and runs on Windows or Linux. > >Vast numbers of molecular graphics programs are advertised for their capability to make "publication quality" images. But what this always seems to refer to is the ability to create stunning color pictures complete with shadows, fog effects, dramatic backgrounds, etc., perhaps rendered with the help of POV-Ray. Nice, but not what I usually need for figures to put into journal articles or technical reports. I usually just want ball-and-stick, black-and-white (or a simple color scheme to highlight heteroatoms), maybe some cross-hatching to suggest depth, and some labeling capability, with the end result a high-resolution image or vector output. > >An example of a program that comes pretty close to what I would like is XChemEdit, where I can read in a structure, and quickly rotate/translate it to a desired orientation. Then, with a few mouse clicks I can remove undesired bonds, make dashed bonds (e.g. for hydrogen bonds or transition states), label bond distances/angles/dihedrals, resize and move labels, etc. This only takes a minute or two, unfortunately the resulting images are not, in my opinion, good enough for external publication. They are nicely labeled and clear, but low-resolution. > >As an alternative, I have tried Schakal99, which can make excellent publication-quality b/w molecular graphics, and it seems that one has extensive control over the final image. But I find it difficult to use even after studying the manual and going through quite a few examples, and I am not sure that certain things like labeling bond angles can even be done. > >I have also looked at XBS, Molden, ORTEP, and WebLab Viewer, but they aren't quite what I am looking for either. We don't own Cache, Chem3D, or Gaussview, so I haven't tried them...what about those or other software? Is it best to just put in the time to really learn Schakal usage? Would you agree that fancy photorealistic "publication quality" graphics are often discouraged by journal editors anyway? > >Thanks! > >Leif Olson >Eastman Kodak Research Laboratories> > > > > From owner-chemistry@ccl.net Wed Jan 11 18:46:00 2006 From: "Dennis G. Sprous dennis.sprous%a%linguagen.com" To: CCL Subject: CCL: Available name-to-structure programs Message-Id: <-30462-060111164302-336-1R4IqcLSQ7t8nU1vHTpwLA . server.ccl.net> X-Original-From: "Dennis G. Sprous" Sent to CCL by: "Dennis G. Sprous" [dennis.sprous:+:linguagen.com] Greetings All: I am interested in name-to-structure conversion programs for databases. The available programs I am aware of are: OpenEyes Lexichem name2mol ACDLabs Name to Structure Batch I realize this is a very difficult problem and I am interested in users experiences with both of these and any other programs that are available. From owner-chemistry@ccl.net Wed Jan 11 19:21:00 2006 From: "forli_-_unisi.it" To: CCL Subject: CCL: Simple molecular graphics Message-Id: <-30463-060111185528-7109-MnBHrtrGKrx3ioJ2o5B+3Q(!)server.ccl.net> X-Original-From: forli]=[unisi.it Date: Wed, 11 Jan 2006 20:13:25 +0200 (MET-DST) Sent to CCL by: forli]|[unisi.it Dear Leif Try Pymol! It's powerful, well supported around the web, support raytrace of nice pics (internally), is easy enough to play with, and it's free. Linux, Mac and Win are supported. http://pymol.sourceforge.net/ Hope this helps, Stefano >Sent to CCL by: "Leif Olson" [leif.olson,,kodak.com] >Hi CCL people, > >I know this is similar to previous questions that have been sent to the list in the past. But I am going to ask it anyway...I keep searching for a program that will make simple publication quality molecular graphics pictures (usually black-and-white), but with a couple of added features, and runs on Windows or Linux. > >Vast numbers of molecular graphics programs are advertised for their capability to make "publication quality" images. But what this always seems to refer to is the ability to create stunning color pictures complete with shadows, fog effects, dramatic backgrounds, etc., perhaps rendered with the help of POV-Ray. Nice, but not what I usually need for figures to put into journal articles or technical reports. I usually just want ball-and-stick, black-and-white (or a simple color scheme to highlight heteroatoms), maybe some cross-hatching to suggest depth, and some labeling capability, with the end result a high-resolution image or vector output. > >An example of a program that comes pretty close to what I would like is XChemEdit, where I can read in a structure, and quickly rotate/translate it to a desired orientation. Then, with a few mouse clicks I can remove undesired bonds, make dashed bonds (e.g. for hydrogen bonds or transition states), label bond distances/angles/dihedrals, resize and move labels, etc. This only takes a minute or two, unfortunately the resulting images are not, in my opinion, good enough for external publication. They are nicely labeled and clear, but low-resolution. > >As an alternative, I have tried Schakal99, which can make excellent publication-quality b/w molecular graphics, and it seems that one has extensive control over the final image. But I find it difficult to use even after studying the manual and going through quite a few examples, and I am not sure that certain things like labeling bond angles can even be done. > >I have also looked at XBS, Molden, ORTEP, and WebLab Viewer, but they aren't quite what I am looking for either. We don't own Cache, Chem3D, or Gaussview, so I haven't tried them...what about those or other software? Is it best to just put in the time to really learn Schakal usage? Would you agree that fancy photorealistic "publication quality" graphics are often discouraged by journal editors anyway? > >Thanks! > >Leif Olson >Eastman Kodak Research Laboratories> > > --- *********************************** Stefano Forli Dip. Farmaco Chimico Tecnologico Universita' degli Studi di Siena Via Aldo Moro I-53100 Siena, Italy Phone: ++39 0577 234307 Fax: ++39 0577 234333 e-mail: forli * unisi.it *********************************** From owner-chemistry@ccl.net Wed Jan 11 19:55:00 2006 From: "Mikael Johansson mikael.johansson[*]helsinki.fi" To: CCL Subject: CCL: Simple molecular graphics Message-Id: <-30464-060111191029-21375-I0K0chKeLNzqgwms3dArRQ:server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Thu, 12 Jan 2006 01:09:51 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson^^helsinki.fi] Hello Leif and All! On Wed, 11 Jan 2006, Leif Olson leif.olson~~kodak.com wrote: > figures to put into journal articles or technical reports. I usually > just want ball-and-stick, black-and-white (or a simple color scheme to > highlight heteroatoms), maybe some cross-hatching to suggest depth, and > some labeling capability, with the end result a high-resolution image or > vector output. Except for the labelling capacity, which is restricted to about atom symbols and numbering, I've found XMakemol to do a good job of the above. It can among other things output black and white as well as colour EPS, so the resolution is naturally good. The EPS it produces is also quite clear, so for example manually editing a colour EPS to grey scale is easy (B/W EPS is really only black and white). http://www.nongnu.org/xmakemol/ Have a nice day, Mikael J. http://www.helsinki.fi/~mpjohans/ From owner-chemistry@ccl.net Wed Jan 11 20:30:01 2006 From: "janl+/-speakeasy.net" To: CCL Subject: CCL: Chemical Computing Group Announces Excellence Award Winners Message-Id: <-30465-060111192900-28212-79D+wtEoVsdLkMydH1JJ7A],[server.ccl.net> X-Original-From: janl]*[speakeasy.net Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 12 Jan 2006 00:28:57 +0000 MIME-Version: 1.0 Sent to CCL by: janl~~speakeasy.net [Resent to Computational Chemistry List by Jan Labanowski] 2006 Press Release Chemical Computing Group Announces "Excellence Award" Winners. MONTREAL, January 11, 2006 - Chemical Computing Group (CCG) and the American Chemical Society's (ACS) Division of Computers in Chemistry (COMP) congratulate winners of the CCG Excellence Awards at the 231st ACS National Meeting in Atlanta, Georgia. The esteemed CCG Excellence Award honors graduate students in the field of computational chemistry. Winners are selected according to the excellence and relevance of their research, as well as the quality of the supporting materials. CCG is proud to award each winner a check to assist with travel and accommodation at the Fall 2006 ACS in Atlanta Georgia, recognition of their award-winning work at the Awards Presentation during the COMP Division Poster Session on Tuesday March 28, 2006, and a one-year software license for the most recent version of MOE - the Molecular Operating Environment. For more information on how to submit for the 2006 ACS Award in San Francisco, please contact Andrew Good at Andrew.Good/a\bms.com 2006 ACS Atlanta Winners: Xhua Chen - New York University Xuhui Huang - Columbia University Casey Kelly - University of Minnesota Valerie McCarthey - University of Pittsburgh Devina Pillay - The University of Texas at Austin Lisa Subissati Chemical Computing Group, Inc 1010 Sherbrooke St. West, Suite 910 Montreal, Quebec H3A 2R7 Tel: 514.393.1055 x 43 Fax: 514.874.9538 http://www.chemcomp.com ----------------------------------------------------- CCG's 3rd User Group Meeting June 27th - 30th, 2006 Montreal, Canada ----------------------------------------------------- From owner-chemistry@ccl.net Wed Jan 11 21:06:01 2006 From: "Jonathan Brecher jsb~!~cambridgesoft.com" To: CCL Subject: CCL: Available name-to-structure programs Message-Id: <-30466-060111205551-26673-1UidyRA/sBPQoQmJHSzGeA:_:server.ccl.net> X-Original-From: Jonathan Brecher Content-Type: text/plain; charset="us-ascii" ; format="flowed" Date: Wed, 11 Jan 2006 19:55:30 -0500 Mime-Version: 1.0 Sent to CCL by: Jonathan Brecher [jsb-$-cambridgesoft.com] Also CambridgeSoft's Name=Struct (available in batch and non-batch versions). Information on the batch version is at http://products.cambridgesoft.com/ProdInfo.cfm?pid=326 I obviously have opinions on the three products, but if you want some useful advice, my suggestion is that you don't take anyone's advice, including mine. Assuming that you are interested in running the software over your own database, the only thing that really matters is how it will fare on the names you actually have. All software has limitations. For example, one specific limitation of CambridgeSoft's software is that it doesn't handle cubane nomenclature. If you happen to have a database of 100,000 cubane derivatives, it doesn't matter how good our software is in the abstract -- it's guaranteed to do you no good at all. (I don't know offhand if any other software handles cubanes, or if your database includes any; that's just an example.) You really need to test how the software handles the data you actually care about, and nobody else can tell you that. You should get demos of all three and try them yourself. Jonathan Brecher CambridgeSoft Corporation jsb~~cambridgesoft.com >Sent to CCL by: "Dennis G. Sprous" [dennis.sprous:+:linguagen.com] > >Greetings All: > >I am interested in name-to-structure conversion programs for databases. >The available programs I am aware of are: > >OpenEyes Lexichem name2mol >ACDLabs Name to Structure Batch > >I realize this is a very difficult problem and I am interested in >users experiences with both of these and any other programs that are >available. From owner-chemistry@ccl.net Wed Jan 11 21:41:01 2006 From: "Jonathan Brecher jsb-#-cambridgesoft.com" To: CCL Subject: CCL: [CCL] Re: CCL: Available name-to-structure programs Message-Id: <-30467-060111210724-5893-IX+YKBGHv7Wf/+0/C13s6g(!)server.ccl.net> X-Original-From: Jonathan Brecher Content-Type: text/plain; charset="us-ascii" Date: Wed, 11 Jan 2006 21:07:09 -0500 Mime-Version: 1.0 Sent to CCL by: Jonathan Brecher [jsb*|*cambridgesoft.com] Also CambridgeSoft's Name=Struct (available in batch and non-batch versions). Information on the batch version is at http://products.cambridgesoft.com/ProdInfo.cfm?pid=326 I obviously have opinions on the three products, but if you want some useful advice, my suggestion is that you don't take anyone's advice, including mine. Assuming that you are interested in running the software over your own database, the only thing that really matters is how it will fare on the names you actually have. All software has limitations. For example, one specific limitation of CambridgeSoft's software is that it doesn't handle cubane nomenclature. If you happen to have a database of 100,000 cubane derivatives, it doesn't matter how good our software is in the abstract -- it's guaranteed to do you no good at all. (I don't know offhand if any other software handles cubanes, or if your database includes any; that's just an example.) You really need to test how the software handles the data you actually care about, and nobody else can tell you that. You should get demos of all three and try them yourself. Jonathan Brecher CambridgeSoft Corporation jsb===cambridgesoft.com >Sent to CCL by: "Dennis G. Sprous" [dennis.sprous:+:linguagen.com] > >Greetings All: > >I am interested in name-to-structure conversion programs for databases. >The available programs I am aware of are: > >OpenEyes Lexichem name2mol >ACDLabs Name to Structure Batch > >I realize this is a very difficult problem and I am interested in >users experiences with both of these and any other programs that are >available.