From chemistry-request@server.ccl.net Thu Jan 4 21:06:59 2001 Received: from web11801.mail.yahoo.com (web11801.mail.yahoo.com [216.136.172.155]) by server.ccl.net (8.8.7/8.8.7) with SMTP id VAA13691 for ; Thu, 4 Jan 2001 21:06:58 -0500 Message-ID: <20010105020655.80401.qmail@web11801.mail.yahoo.com> Received: from [162.105.177.30] by web11801.mail.yahoo.com; Fri, 05 Jan 2001 10:06:55 CST Date: Fri, 5 Jan 2001 10:06:55 +0800 (CST) From: =?gb2312?q?Malin=20Liu?= To: chemistry@www.ccl.net, chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear CCLers, Does anyone know what's the standard bond energy of S-S between CYX-CYX in proteins? (experiment result or theoretical calculating result, please point out the reference books or journal papers). Any references will be appreciated, thanks a lot. Malin _________________________________________________________ Do You Yahoo!? 登录免费雅虎电邮! http://mail.yahoo.com.cn 创建雅虎俱乐部，真我个性尽施展！http://cn.clubs.yahoo.com From chemistry-request@server.ccl.net Fri Jan 5 08:16:49 2001 Received: from fletxa.iqs.es (root@[193.145.86.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA17071 for ; Fri, 5 Jan 2001 08:16:48 -0500 Received: from millet (millet.iqs.url.es [193.145.86.12]) by fletxa.iqs.es (8.9.3/8.9.3) with SMTP id OAA30789 for ; Fri, 5 Jan 2001 14:45:26 +0100 Message-ID: <002501c07721$d6e96520$0c5691c1@iqs.url.es> Reply-To: "Oscar Rey" From: "Oscar Rey" To: Subject: Angle force constants Date: Fri, 5 Jan 2001 14:14:32 -0000 Organization: Iqs Dear colleagues: I'm trying to develop some new AMBER parameters for my molecules. I have some problems to develop the angle force constants from the hessian matrix. I've read the AMBER home page but I only got information about calculating bond distance force constant. Does anybody know any reference about it or how to do it? Thanks in advance! Oscar Rey Puiggros Computational Chemistry Group, Molecular Engineering Group (GEM) Institut Quimic de Sarria (Ramon Llull University) Barcelona From chemistry-request@server.ccl.net Fri Jan 5 09:21:28 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA17423 for ; Fri, 5 Jan 2001 09:21:28 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id JAA18988; Fri, 5 Jan 2001 09:21:14 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Fri, 05 Jan 2001 09:20:32 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0G6P00K20115AL@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Fri, 05 Jan 2001 09:17:29 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Fri, 05 Jan 2001 09:20:28 -0500 Content-return: allowed Date: Fri, 05 Jan 2001 09:20:21 -0500 From: "Shobe, Dave" Subject: Gamess equiv of lanl2dz To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629DDAABA1@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id JAA17424 What is the equivalent in Gamess of what Gaussian calls LANL2DZ ? I need both the ECP and the basis set. --David Shobe S黡-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com From chemistry-request@server.ccl.net Fri Jan 5 10:08:37 2001 Received: from dual.fqspl.com.pl (dual.fqspl.com.pl [212.244.147.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA17661 for ; Fri, 5 Jan 2001 10:08:36 -0500 Received: from victor (victor.fqspl.com.pl [10.10.10.5]) by dual.fqspl.com.pl (8.11.1/8.11.1) with SMTP id f05GGA723546; Fri, 5 Jan 2001 17:16:10 +0100 Message-ID: <003d01c07728$e9f68ba0$050a0a0a@fqspl.com.pl> From: "Victor Anisimov" To: "Oscar Rey" , References: <002501c07721$d6e96520$0c5691c1@iqs.url.es> Subject: Re: CCL:Angle force constants Date: Fri, 5 Jan 2001 16:05:17 +0100 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi Oscar, I can recommend you looking into GAMESS US. It has a function of converting Cartesian Force constant matrix into internal coordinates. This way you will get force constants of bonds, angles and torsions calculated. As you know there is no strict way of obtaining force constant related to particular internal coordinate for many-atom molecule but at least the method used in GAMESS is the best a theory can suggest now. If you will find anything better I'd be very interested getting your summary. GAMESS manual has a few references pointing onto original publications regarding this conversion of Force constant matrix. If you have Gaussian, GAMESS, or MOPAC2000 Force constants calculated you may take a look onto ISOEFF98 program that will help you playing with different Z-matrix and will do for you this conversion of Cartesian force constants into internal coordinate representation. The program is designed for isotope effect calculation but you may find it useful for your case too. A Web site of ISOEFF98 is: http://ck-sg.p.lodz.pl/isoeff/isoeff.html The program is distributes as open source, so you can compile it under any platform. Windows and Linux binaries are available too. Any feedbacks about the program are welcome. In case you need any help do not hesitate to contact me. With regards. Victor. ========================================================================== Victor Anisimov, PhD, Senior Software Researcher - Computational Chemist FQS Poland, ul. Starowislna 13-15, 31-038 Krakow, Poland Email: victor@fqspl.com.pl Tel.(+48 12) 429-4345 Fax(+48 12) 429-6124 ========================================================================== ----- Original Message ----- From: Oscar Rey To: Sent: Friday, January 05, 2001 3:14 PM Subject: CCL:Angle force constants > Dear colleagues: > > I'm trying to develop some new AMBER parameters for my molecules. I have > some problems to develop the angle force constants from the hessian > matrix. > I've read the AMBER home page but I only got information about > calculating bond distance force constant. Does anybody know any > reference about it or how to do it? > > Thanks in advance! > > Oscar Rey Puiggros > Computational Chemistry Group, Molecular Engineering Group (GEM) > Institut Quimic de Sarria (Ramon Llull University) > Barcelona > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > From chemistry-request@server.ccl.net Fri Jan 5 11:39:39 2001 Received: from server3.safepages.com (server3.safepages.com [216.127.146.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA18197 for ; Fri, 5 Jan 2001 11:39:39 -0500 Received: from kressj (5131-196-251.008.popsite.net [209.69.196.251]) by server3.safepages.com (Postfix) with SMTP id 0443423441; Fri, 5 Jan 2001 16:38:54 +0000 (GMT) Message-ID: <002901c07735$fe825420$0100a8c0@webrise.net> From: "Jim Kress" To: "Shobe, Dave" , "'CCL'" References: <157A51F55AAAD3119CD70008C7B1629DDAABA1@lvlxch01.unitedcatalysts.com> Subject: Re: CCL:Gamess equiv of lanl2dz Date: Fri, 5 Jan 2001 11:38:48 -0500 Look here: http://www.emsl.pnl.gov:2080/forms/basisform.html and specify lanl2dz and the element(s) of interest. Jim ----- Original Message ----- From: "Shobe, Dave" To: "'CCL'" Sent: Friday, January 05, 2001 9:20 AM Subject: CCL:Gamess equiv of lanl2dz > What is the equivalent in Gamess of what Gaussian calls LANL2DZ ? I need > both the ECP and the basis set. > > --David Shobe > S黡-Chemie Inc. > phone (502) 634-7409 > fax (502) 634-7724 > email dshobe@sud-chemieinc.com From chemistry-request@server.ccl.net Fri Jan 5 13:34:12 2001 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA18693 for ; Fri, 5 Jan 2001 13:34:12 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id NAA16570; Fri, 5 Jan 2001 13:33:56 -0500 (EST) Date: Fri, 5 Jan 2001 13:33:56 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: Free CAChe Seminars Jan 30, 31, Feb Princeton, New Haven, Boston Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII From: Tamara Palmer Subject: Free CAChe Seminars CAChe Seminar Announcement: "Prediction of Physical, Chemical, and Biological Properties with Computer Aided Chemistry" (includes QSAR/QSPR and Reaction Modeling) * Tuesday, January 30th, 10:00am, Princeton, NJ * Wednesday, January 31st, 3:00pm, New Haven, CT * Thursday, February 1st, 9:00am, Cambridge, MA** (Feb 1 only: joint seminar with CambridgeSoft.Com) Abstract and further information from: http://www.cachesoftware.com/news/seminars2000.shtml Please contact Tamara at tpalmer@cachesoftware.com or (503)746-3610 to register, or if you would like to be notified of future CAChe seminars in your area. These seminars are sponsored by Fujitsu and CambridgeSoft**. From chemistry-request@server.ccl.net Fri Jan 5 13:36:49 2001 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA18738 for ; Fri, 5 Jan 2001 13:36:48 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id NAA16706 for ; Fri, 5 Jan 2001 13:36:33 -0500 (EST) Date: Fri, 5 Jan 2001 13:36:33 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net Subject: MOPAC & CAChe - Seminars in Poland - Jan 18 & 19, 2001 (fwd) Message-ID: Date: Thu, 4 Jan 2001 21:26:39 -0000 From: Jerzy M Rudzinski Subject: MOPAC and CAChe - Seminaria w Polsce - Styczen 2001 Computer Aided Chemistry (CAChe) and MOPAC2000 Seminar Sponsored by Fujitsu and local hosts 18 -19 January 2001, Poland The Seminar includes two one-hour lectures followed by a brief software demonstration: "Prediction of physical, chemical, and biological properties with computer aided chemistry" by David Gallagher Vice President, CAChe Group Fujitsu Systems Business of America and "State of the Art Quantum Mechanics - MOPAC2000" by Dr. James J.P. Stewart Fujitsu Consultant Stewart Computational Chemistry Seminar Schedule: 18 January 2001 (Thursday) 10:00 Gdansk Wydzial Chemii - Sala 112 Uniwersytet Gdanski Ul. Sobieskiego 18, 80-952 Gdansk Local Host: Dr. Stanislaw Oldziej (stan@chemik.chem.univ.gda.pl) Tel (058)-345-0361 Fax (058)-341-0357 19 January 2001 (Friday) 10:30 Warszawa Sala Konferencyjna Instytut Chemii Organicznej, Kasprzaka 44/52 Polska Akademia Nauk (Polish Academy of Sciences) Local Host: Prof. Marek Pietraszkiewicz (pietrasz@ichf.edu.pl) Tel (022) 6323221 wew. 3201 Fax (022) 6325276 REGISTRATION: Attendance is free, but accommodation is limited. To reserve your place and the Seminar Material set please register the date required, your name, company, address and telephone number with Marta Derleta at marta@fqspl.com.pl or phone (012) 429 43 45 by 15th January 2000. Alternatively you can register by fax to: (012) 429 6124 or by contacting local host of the seminar site chosen. Note on the Seminar: Prediction of physical, chemical, and biological properties with computer aided chemistry Presenter: David A. Gallagher, C.Chem., CAChe Group, Fujitsu. The prediction of biological, chemical and physical properties such as reaction rates, UV-Visible & IR spectra, water solubility, vapor pressure, polymer properties, carcinogenicity, environmental fate, etc., etc. will be illustrated with CAChe, an easy-to-use computer aided chemistry package for the experimental chemist that runs on a desktop PC. Prediction of reaction pathways, thermodynamics and kinetics will also be discussed as well as application to quantitative structure-property relationships (QSPR & QSAR). Chemists use CAChe to improve their success rate in the laboratory and speed up research by prescreening candidates and testing their ideas, before investing valuable laboratory time. This presentation reviews the expanding scope of computer aided chemistry. State of the Art Quantum Mechanics - MOPAC2000 Presenter: Jimmy J.P. Stewart, Stewart Computational Chemistry - author of MOPAC In recent years, many advances have taken place in the semi-empirical computational chemistry program MOPAC. The most recent form, MOPAC2000, has some 40 new features. This presentation will focus on a few of these features: 1. Use of Dynamic Memory Allocation. 2. MNDO-d and AM1-d (including transition metals and their complexes). 3. The new linear scaling algorithm MOZYME, and some applications to proteins and other systems. 4. Excited states in solution. 5. The lowering of activation energies by intersystem crossing. 6. Modeling of different types of solids, and investigation of electronic phenomena in solids. The direction of future research efforts will be indicated. ---------------------------------------------------------------------------- ------------------------------- =============================================== Jerzy M Rudzinski,PhD FQS Poland Sp. z o.o. ul.Starowislna 13-15 31-038 Krakow Poland Phone: (+48 12) 429 4345 Fax: (+48 12) 429 6124 Email: jerzy@fqspl.com.pl URL: www.fqspl.com.pl =============================================== From chemistry-request@server.ccl.net Fri Jan 5 14:10:53 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA18868 for ; Fri, 5 Jan 2001 14:10:52 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id OAA30697; Fri, 5 Jan 2001 14:10:51 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Fri, 05 Jan 2001 14:10:07 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0G6P00LNFEFUGK@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Fri, 05 Jan 2001 14:07:06 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Fri, 05 Jan 2001 14:10:04 -0500 Content-return: allowed Date: Fri, 05 Jan 2001 14:09:57 -0500 From: "Shobe, Dave" Subject: Gamess--thanks To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629DDAABA4@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id OAA18869 Thanks to all who helped with my questions about downloading Gamess* and the basis set/ecp lanl2dz.** Downloading Gamess wasn't so bad--only 3MB in the zipped form. As for LANL2DZ, basically you all pointed me to the web site http://www.emsl.pnl.gov:2080/forms/basisform.html, and sure enough LANL2DZ is there, ECP and all. *Karl Irikura, Jim Kress, Deepak Singh, Slawomir Janicki **Alexander Hofmann, Matthias Hofmann, Sean Hughes, Frederick Arnold, Fedor Goumans, Jim Kress (If I left anyone out, I apologize. :-) --David Shobe S黡-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com From chemistry-request@server.ccl.net Fri Jan 5 14:11:01 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA18880 for ; Fri, 5 Jan 2001 14:11:01 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id OAA30753; Fri, 5 Jan 2001 14:11:00 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Fri, 05 Jan 2001 14:10:17 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0G6P00LNIEG4GK@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Fri, 05 Jan 2001 14:07:16 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Fri, 05 Jan 2001 14:10:14 -0500 Content-return: allowed Date: Fri, 05 Jan 2001 14:10:04 -0500 From: "Shobe, Dave" Subject: More ?? about Gamess and comparability To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629DDAABA5@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id OAA18881 I do have a few generalizations of the LANL2DZ question I asked earlier though. First, if the Gamess and Gaussian manuals' references for the basis set match, can I assume they are identical (at least for elements supported by both programs)? And second, if I run "the same" calculation in Gamess and Gaussian, should I expect the same energy? What pitfalls should I expect (I mean things like full vs. frozen-core for example)? --David Shobe S黡-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com From chemistry-request@server.ccl.net Fri Jan 5 15:19:43 2001 Received: from markov.chem.rochester.edu (markov.chem.rochester.edu [128.151.176.16]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA19340 for ; Fri, 5 Jan 2001 15:19:43 -0500 Received: (from serg@localhost) by markov.chem.rochester.edu (8.10.1/8.10.1) id f06KJhh09807; Fri, 6 Jan 2001 15:19:43 -0500 (EST) Date: Fri, 6 Jan 2001 15:19:43 -0500 (EST) From: Sergei Tretiak To: "'CCL'" Subject: Summary: Crystal structure and XYZ coordinates Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Thanks to all who helped with my questions about Crystal structure and XYZ coordinates This is the summary of the responses. Thanks again. Sincerely, Sergei .-----------------------------------------------------------------------. |\ / \ | Sergei Tretiak | / \ /| |.\/...\|.......................................................|/...\/.| | Theoretical Division | Voice: (505) 667-8351 | | Mail stop B262 | Fax: (505) 665-4063 | | Los Alamos National Lab | E-mail: serg@markov.chem.rochester.edu | | Los Alamos, NM 87545 | serg@wigner.chem.rochester.edu | | Homepage: http://markov.chem.rochester.edu/serg/welcome.html | |_______________________________________________________________________| Original request: > Dear Netters: > > Suppose I have cell parameters and would like to > build a piece of crystal and save Cartesian coordinates > of atoms that will be inside of sphere (ellipsoid, cube, > etc.) with given radius. > > What software (free or commercial) could do that? (Easy to > use, options, good visualization capability would be preferences). Responses: __________________________________________________________ From: "Anatoli Korkin (r40757)" The MSI crystal bulider does the best for that purpose. http://www.msi.com/ Cheers, Anatoli __________________________________________________________ From: Jeffery Brian Klauda I would try Diamond version 2. You can go to their website, which is listed below. The demo version can build structures and save them in cartesian coordinates as well as save selected atoms in a sphere or cube. http://www.crystalimpact.com/diamond/ Hope this helps, Jeff Klauda __________________________________________________________ From: Alexander Hofmann I know MSI Cerius2, which is capable to cut spheres (no intrinsic ellipsoids) and rectangular bodies with its GUI. You can save your modified file into various formats. (commercial: www.msi.com) Another idea is to use a program like xmol or jmol (the java version of it) to edit a prebuilt supercell. (free: http://www.msc.edu/msc/docs/xmol/ftp.html )only very old architectures) and http://www.openscience.org/jmol/index.html) Hope this helps Alex __________________________________________________________ From: "Students of Dr. S. R. Gadre" I think MSI's Weblab-viewer pro would be good enough for that. you can look at www.msi.com for pricing and further details Babu __________________________________________________________ From: Victor Milman You can use Materials Studio from MSI which allows you to select atoms that are within a given distance from the selected atoms (or from a specified point in space). You can also select atoms that have X, Y, or Z that satisfy one of the criteria: Equal To, Greater Than, Less Than, Greater Than or Equal To, Less Than or Equal To, Inclusive Range, or Exclusive Range. The same will work for X, Y, Z relative to coordinates of the selected atoms. I think you can combine these features to achieve your goal of selecting atoms within a sphere or a cube (which is presumably to apply cluster-based quantum chemistry methods to study periodic solids - I am not a great fan of this approach). After you selected what you wanted, you can copy these atoms into another model space (MatStudio supports all then usual cut/copy/paste). alternatively you can invert selection criteria, select only what you don't want and delete those atoms. You can find out more about Materials Studio at http://www.msi.com/materials/studio/ and about other offerings from MSI at http://www.msi.com/materials/index.html Hope this helps __________________________________________________________ David Gallagher CAChe includes a crystal builder with all 230 space groups. You select the space group from a pull-down menu and it highlights which parameters are needed. You can paste in or type in the fractional coordinates and then define the size and type of the crystal to be built along each of the three axes. CAChe can also read Shel-X, Cambridge, etc. directly, and handles all elements up to 103. CAChe has won several awards for ease-of-use. The excellent visualization includes coordination polyhedra, thermal ellipsoids and optional full-color stereoscopic. The crystal builder is in all versions of CAChe including Personal CAChe on Windows and Mac at $495 for academics. You can download a free evaluation copy from www.cachesoftware.com or call 503 531 3600 for a CD and any questions. Hope this helps, happy new year, David Gallagher __________________________________________________________ From: Didier MATHIEU To convert the asymmetric cell into the orthorhombic cell, the crystal program of the Tinker package is useful: http://dasher.wustl.edu/tinker Not all space groups are implemented, but it is easy to has additional ones. Then I can copy the unit cell obtained along the X,Y,Z axes to get a model cluster. It would be easy then to check for the atoms belonging to a shere, ellipsoid... > use, options, good visualization capability would be preferences). For visualization I use XMol but tinker provides an utility to generate .pdb files that can be read by most vizualization packages (e.g. VMD). Regards -- Didier Mathieu