From - Fri May 02 15:35:21 1997 Message-ID: <336A41F9.D8B@hyper.com> Date: Fri, 02 May 1997 15:35:21 -0400 From: Krassimir Stavrev Organization: Hypercube, Inc. X-Mailer: Mozilla 3.0 (Win95; I) MIME-Version: 1.0 To: hyperchem@hyper.com Subject: New Macros Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mozilla-Status: 0001 Content-Length: 1183 Dear HyperChemists, We have two new macros available thanks to Dr. Laszlo JICSINSZKY now downloadable from our software archive, http://www.hyper.com/Software/Other/other_index.html. Each macro is supplied by a short readme-file, again courtesy of Laszlo. The first macro, NewOpen, explores Visual Basic as an alternative to the Excel macros available through the HyperChem manuals. It is simple and easy to use. The second macro, NewCage, creates a cage of solvent molecules /user's choice/ setting them in a solvation box in a way similar to that implemented in HyperChem. The solute has to be brought manually in the box and subsequently relaxed in the solvation shell. This macro has no limitations to solvents and can be used as a starting model for non-aqueous solutions. An explanation of these utilities can also be found in the April'97 summary in our User's Group Archive. We will welcome your feedback. Regards, Krassimir --- Krassimir Stavrev, PhD Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice: 1-352-371-7744/1-800-960-1871 Fax: 1-352-371-3662 From - Mon May 05 08:56:13 1997 Date: Sun, 4 May 1997 19:12:19 +0200 (MET DST) From: Sandy Yates To: hyperchem@hyper.com Subject: A book. In-Reply-To: <11060BD0FC6@virgil.ruc.dk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Mozilla-Status: 0001 Content-Length: 761 Hi, I am intersted if anybody has any comment on the following book. The title appears to be very interesting. Does any body know what the scope and contents are. I found it by chance at www.amazon.com the online bookstore. "Ab Initio Variational Calculations of Molecular Vibrational-Rotational Spectra" (Lecture Notes in Chemistry, Vol 61) $57 by D. Searles, E. Von Nagy-Felsobuki SANDY ------------------------------------------------------------------------ Sandy Yates / Area de Mecanica de Fluidos / Centro Politecnico Superior Maria de Luna, 3 / 50015 ZARAGOZA. SPAIN Phone: Spain +34 76 761000 ext 5045. Fax: Spain +34 76 761882 Email: sandy@ideafix.cps.unizar.es From - Mon May 05 15:01:08 1997 From: ZHANGX1@miavx1.acs.muohio.edu Date: Mon, 05 May 1997 13:00:40 -0500 (EST) Subject: charge distribution To: hyperchem@hyper.com Message-id: <01IIIFT80EF296VVKH@miavx1.acs.muohio.edu> MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII X-Mozilla-Status: 0001 Content-Length: 872 I'm currently doing molecular dynamics calculation on multiply protonated peptide ions using Bio+ force field. One problem I'm encounting is that I don't know how to change the number of protons the ion bears (by default it will equal to the number of basic residues in the peptides, but sometimes I need to perform calculations on less than fully protonated forms). Also I don't know how to smooth the charge over the the molecular ion. By using Bio+, every atom in the peptide ion will carry some sort of average charge number, after adding or removing H atom on some residues (for the purpose to change the position or number of protons in the ion), I don't know how to re-smooth the charge over the ion (or how to assign the charge on the atoms being added). Any suggestion or comments regarding this problem will be appreciated. Thank you very much. From - Mon May 05 18:16:33 1997 Message-ID: <336E5C40.39E0@hyper.com> Date: Mon, 05 May 1997 18:16:33 -0400 From: Krassimir Stavrev Organization: Hypercube, Inc. X-Mailer: Mozilla 3.0 (Win95; I) MIME-Version: 1.0 To: ZHANGX1@miavx1.acs.muohio.edu CC: joelp@agiss.com Subject: Re: charge distribution References: <01IIIFT80EF296VVKH@miavx1.acs.muohio.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mozilla-Status: 0011 Content-Length: 1574 ZHANGX1@miavx1.acs.muohio.edu wrote: > > I'm currently doing molecular dynamics calculation on multiply protonated > peptide ions using Bio+ force field. One problem I'm encounting is that I > don't know how to change the number of protons the ion bears (by default it > will equal to the number of basic residues in the peptides, but sometimes I > need to perform calculations on less than fully protonated forms). Also I > don't know how to smooth the charge over the the molecular ion. By using Bio+, > every atom in the peptide ion will carry some sort of average charge number, > after adding or removing H atom on some residues (for the purpose to change the > position or number of protons in the ion), I don't know how to re-smooth the > charge over the ion (or how to assign the charge on the atoms being added). > Any suggestion or comments regarding this problem will be appreciated. Thank > you very much. > Hi, You posed an interesting question. Perhaps Joel knows more about charge effects on various force fields. I have been wondering this too, playing recently with acetone and its structural properties depending on the O-atom lone pairs. It seems that their presense and positioning has a large effect on the C-O-C bridge and overall properties. The same should apply to protonation I believe. Regards, Krassimir --- Krassimir Stavrev, PhD Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice: 1-352-371-7744/1-800-960-1871 Fax: 1-352-371-3662 From - Tue May 06 08:35:48 1997 Date: Tue, 6 May 1997 10:29:03 +0200 (MDT) From: "Modelling '97" To: chem-com@mailbase.ac.uk, chem-mod@mailbase.ac.uk, chemistry@osc.edu, ipmdg-l@venus.co.uk, amber@cgl.ucsf.edu, c2-l@msi.com, cache@pacificu.edu, charmm-bbs@emperor.harvard.edu, hyperchem@hyper.com, mmodinfo@uoft02.utoledo.edu, quanta-l@msi.com, sybyl@extreme.chem.rpi.edu, watoc@ic.ac.uk Subject: MGMS Bursaries : Model(l)ing '97 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Mozilla-Status: 0001 Content-Length: 1429 The Molceular Graphics and Modelling Society (MGMS) is pleased to announce that it will be awarding a total of eight bursaries for young scientists for the Model(l)ing '97 conference in Erlangen, Germany, from 2-5 Sept. 1997. For details of the conference see: http://www.organik.uni-erlangen.de/model97 Bursaries will be awarded to graduate students or postdocs who give a lecture or present a poster at the conference. Note that the deadline for lecture submissions (originally May 1st) has been extended to June 1st to allow applications for bursaries. The deadline for poster submissions from bursary-applicants is also June 1st, not July 1st as for other posters. The bursaries will include conference regstration, accomodation in an economy room and a contribution towards travel expenses. Applications should be via the electronic registration facility availble through the above URL and should be accompanied by a recommendation from the supervisor emeiled to model97@organik.uni-erlangen.de Decisions as to the winners of the bursaries will be announced on June 1st. ----- Model(l)ing '97 Computer Chemie Centrum - Institut f. Organische Chemie I Naegelsbachstrasse 25 - D-91052 Erlangen Deutschland / Germany Tel: 0049-9131 - 85 6581 Fax: 0049-9131 - 85 6565 E-Mail: model97@organik.uni-erlangen.de WWW: http://www.organik.uni-erlangen.de/model97/ From - Thu May 08 07:55:51 Message-ID: <3372207E.1BDC@L30.itim-cj.ro> Date: Thu, 08 May 1997 11:50:38 -0700 From: "Sorin V. Filip" Organization: Institute of Isotopic and Molecular Technology Cluj-Napoca X-Mailer: Mozilla 3.0Gold (Win16; I) MIME-Version: 1.0 To: hyperchem@hyper.com Subject: subscribe Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mozilla-Status: 0001 Content-Length: 261 subscribe -- Sorin V. FILIP Institute for Isotopic and Molecular Technology Molecular Physics Lab. 65-103 Donath St., P.O.Box 700 RO-3400, Cluj-Napoca 5 ROMANIA tel. : +40-64-184037 / 223 fax. : +40-64-420042 e-mail : svfilip@L30.itim-cj.ro From - Fri May 09 08:05:09 1997 Comments: Authenticated sender is From - Thu May 08 07:55:51 Message-ID: <3372207E.1BDC@L30.itim-cj.ro> Date: Thu, 08 May 1997 11:50:38 -0700 From: "Sorin V. Filip" Organization: Institute of Isotopic and Molecular Technology Cluj-Napoca X-Mailer: Mozilla 3.0Gold (Win16; I) MIME-Version: 1.0 From: "Thomas Futterer" Organization: Universitaet Regensburg To: info@hyper.com Date: Thu, 8 May 1997 21:19:25 +0200 Subject: question about ZINDO Priority: normal Dear Hyperchemists, can you help me ...? I did the following ZINDO/1 calculation on hyperchem 4.5 for SGI: I calculated a positive charged silver-pi-system-complex (for example silver(+)-ethene-complex: after geometry opt. heat of formation -811 kcal/mol) I deleted the silver-ion and did a single point calculation on the uncharged ethene (heat of formation -896 kcal/mol) I made a analog calculation for the charged Ag(+) (heat of formation +237 kcal/mol) when you calculate the energy for the solvatation-process for the Ag+-Ion you get: -811 kcal + 896 kcal -237 kcal = -152 kcal (/mol) For the process (Z)Stilbene reacts with Ag+, you get -485 kcal/mol QUESTION: These energies seem to be TOO high for the energy of coordination of Ag(+) to pi-ligands like ethene .... Do you have any explanation for these large energies? Did I somethig wrong or shall I change kcal to kJ, this seem to result in more convenient values... Thank you for reading this, if you are not responsible for answering this, would you please be so kind and forward this to sombody who might know ? Thomas _________________________________________________ Dipl.-Chem Thomas Futterer Prof.Dr.A.Merz Institut fuer Organische Chemie der Universitaet Regensburg Universitaetsstrasse 31 D-93053 REGENSBURG,Germany Phone: (+) 49 941 943 4650 Fax: (+) 49 941 943 4505 Email: thomas.futterer@chemie.uni-regensburg.de From - Fri May 09 12:32:21 1997 Message-ID: <33735195.15AB@hyper.com> Date: Fri, 09 May 1997 12:32:21 -0400 From: Krassimir Stavrev Organization: Hypercube, Inc. X-Mailer: Mozilla 3.0 (Win95; I) MIME-Version: 1.0 To: thomas.futterer@chemie.uni-regensburg.de Subject: Re: question about Zindo Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mozilla-Status: 0011 Content-Length: 1583 Hi Thomas, Zindo is known to do a lousy job on thermodynamics. I hate to say that as I, myself, was a contributor to Mike Zerner's Zindo, but coordination estimates like the one you obtained are frequent, especially when atoms of heavier metals are involved. The reason for this is that Zindo was parametrized to get either the spectroscopy (/S), or the geometry (/1) right, but never the heats of formation as a separate issue. There might be a progress in this area, however, as they want this project done by someone at Zerner's group soon. I'll keep the HyperChem's newsgroup posted on this suject. Just to reproduce your experiment, here are the UHF total energies I obtained: Ag+ and C2H4 = -1417.02 (kcal/mol) C2H4 (single point) = -1436.66 C2H4 (optimized) = -1446.15 Ag+ = 168.58 The estimated net effect of this reaction is -149 or -139 kcal/mol, depending on the C2H4 choice (most people prefer the optimized one, although it does not change the order of esti- mate). Basically this is the result you get. You see from the first 2 lines how small is the total energy differece between the coor- dinated and uncoordinated C2H4 (~20 kcal/mol) and then it comes up with a large number for the Ag ion which is an order of magnitude larger than that expected from above... Regards, Krassimir --- Krassimir Stavrev, PhD Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice: 1-352-371-7744/1-800-960-1871 Fax: 1-352-371-3662 From - Mon May 12 08:31:45 1997 Date: Sun, 11 May 1997 19:39:26 +0100 (BST) From: patrick kane <94970459@tolka.dcu.ie> To: CCL Every , HChem User , HChem Supp Subject: HyperChem, AM1 and Phosphorous-Oxygen Bonds Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Mozilla-Status: 0001 Content-Length: 844 Hi, On Page 122 of the HyperChem Computational Chemistry Manual, v. 4.0, it is stated that treatment of phosphorous-oxygen bonds with the AM1 semi-empirical (SE) method is inaccurate. However, I cannot find a reference for this statement. Could someone please point me to an appropriate article. Furthermore, can anyone suggest what is the most appropriate SE method? Thanks in advance for any help. Kind Regards, Paddy. ************************************************************************* * * * Paddy Kane email: 94970459@tolka.dcu.ie * * School of Chemical Sciences * * Dublin City University Tel: 00-353-1-7045641 * * Dublin 9 * * Ireland. Fax: 00-353-1-7045503 * * * ************************************************************************* From - Mon May 12 11:11:46 1997 Message-ID: <33773331.1006@hyper.com> Date: Mon, 12 May 1997 11:11:46 -0400 From: Krassimir Stavrev Organization: Hypercube, Inc. X-Mailer: Mozilla 3.0 (Win95; I) MIME-Version: 1.0 To: patrick kane <94970459@tolka.dcu.ie>, hyperchem@hyper.com Subject: Re: HyperChem, AM1 and Phosphorous-Oxygen Bonds References: Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mozilla-Status: 0011 Content-Length: 2393 patrick kane wrote: > > Hi, > > On Page 122 of the HyperChem Computational Chemistry Manual, v. 4.0, it > is stated that treatment of phosphorous-oxygen bonds with the AM1 > semi-empirical (SE) method is inaccurate. > > However, I cannot find a reference for this statement. Could someone > please point me to an appropriate article. > > Furthermore, can anyone suggest what is the most appropriate SE method? > > Thanks in advance for any help. > > Kind Regards, > Paddy. > > ************************************************************************* > * * > * Paddy Kane email: 94970459@tolka.dcu.ie * > * School of Chemical Sciences * > * Dublin City University Tel: 00-353-1-7045641 * > * Dublin 9 * > * Ireland. Fax: 00-353-1-7045503 * > * * > ************************************************************************* Paddy, AM1 is generally the best of the Dewar’s group of SE methods that was developed and thoroughly tested on various compounds. Phosphorus, however, seem to be a problem, as AM1 is known to distort symmetrical PxOy groups and predict quite different P-P bonds, see J.Stewart in J. Computer-Aided Mol. Design 4 (1990) 1. See also Dewar et al. J. Mol. Struct. (Theochem) 187 (1989) 1. Previously, MINDO/3 was successfully used for third row atoms, including phosphorus, and the reference to this work is Dewar et al., J.Am.Chem.Soc. 97 (1975) 1311; perhaps others who have experience with phosphorus compounds can add to this. A good overview of these methods can be found in Michael Dewar’s article in Int. J. Quant. Chem. 44 (1992) 427-447. Another good source of information about SE methods and com- parisons is J. Stewart’s review in Reviews of Computational Chemistry (1990), p.45-81, and the MOPAC’s documentation. Regards, Krassimir --- Krassimir Stavrev, PhD Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice: 1-352-371-7744/1-800-960-1871 Fax: 1-352-371-3662 From - Wed May 14 09:08:56 1997 Message-ID: <3379B968.15DF@hyper.com> Date: Wed, 14 May 1997 09:08:56 -0400 From: Krassimir Stavrev Organization: Hypercube, Inc. X-Mailer: Mozilla 3.0 (Win95; I) MIME-Version: 1.0 To: ZHANGX1@miavx1.acs.muohio.edu Subject: Re: charge distribution Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mozilla-Status: 0011 Content-Length: 2029 Hi, I received an expert opinion on your problem which came from Joel Polowin who worked with MM a lot before. I enclose his comments here. Regards, Krassimir --- Krassimir Stavrev, PhD Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice: 1-352-371-7744/1-800-960-1871 Fax: 1-352-371-3662 >> I'm currently doing molecular dynamics calculation on multiply protonated >> peptide ions using Bio+ force field. One problem I'm encounting is that I >> don't know how to change the number of protons the ion bears (by default it >> will equal to the number of basic residues in the peptides, but sometimes I >> need to perform calculations on less than fully protonated forms). Some of the residues have multiple forms with different numbers of protons. If this is true for the residues this fellow is using, he can make the change with the Mutate function. Or, of course, he can delete the atoms manually. >> Also I >> don't know how to smooth the charge over the the molecular ion. By using Bio+, >> every atom in the peptide ion will carry some sort of average charge number, >> after adding or removing H atom on some residues (for the purpose to change the >> position or number of protons in the ion), I don't know how to re-smooth the >> charge over the ion (or how to assign the charge on the atoms being added). If he can use different residues, they will have correct charges. Alternately, there's the Set Charge function, which would be applied to the atoms one at a time. If his structure is small, charges can be calculated by Extended Huckel or by one of the other QM methods. He also has the option of creating his own modified residues in the template file, with whatever charges he wants. That's much more difficult; changing the templates is hard to figure out. I'd suggested that HyperChem could use a Residue/Template editor, but again, that wasn't a very high priority. Regards, Joel From - Wed May 14 10:22:31 1997 From: ACCOMAZZ@ICIL64.CILEA.IT Date: Tue, 13 May 1997 11:04:55 +0000 (MET-01DST) Subject: File conversion utility requested To: hyperchem@hyper.com Message-id: <01IITHG6MIJM00726C@ICIL64.CILEA.IT> X-VMS-To: IN%"hyperchem@hyper.com" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII X-Mozilla-Status: 0001 Content-Length: 954 Hello I'm looking for a file conversion utility from the MSI (BioSym or Insight) .car / .mdf file format to HyperChem (.hin) file format. We have HyperChem running on PC's and MSI (BioSym or Insight) on SGI Workstations. The problem is how to quicly exchange data and how to read our structures archive made of files in .car/mdf format. The procedure we use now is to read and save .hin and .car/.mdf in MDL .mol format, which is readable / writable from both Hyperchem / MSI (BioSym). The most interesting file conversion program I found on the Internet is >MOL2MOL -- an easy-to-use file conversion program for the chemist but it can't read directly .car / .mol files. If anyone has any kind of information that can help me please contact me by email directly at this address: accomazz@icil64.cilea.it ================================ Dr. Paolo Accomazzi EniChem - Centro Ricerche Novara via Fauser, 4 28100 NOVARA ITALY From - Wed May 14 10:22:31 1997 From: steve_rogers@ici.co.uk X400-Originator: steve_rogers@ici.co.uk X400-Recipients: hyperchem@hyper.com X400-MTS-Identifier: [/PRMD=ICI/ADMD=TMAILUK/C=GB/;0031900002905653000002] X400-Content-Type: P2-1988 (22) Message-ID: <0031900002905653000002*@MHS> To: " - (052)hyperchem (a) hyper.com" Subject: ESP surfaces in HyperChem 5 Date: Tue, 13 May 1997 15:46:47 +0100 X-Mozilla-Status: 0001 Content-Length: 629 Dear Krassimir, Joel ..., I am evaluating HyperChem 5 (Windows 95 version). I am very interested in the mapping of electrostatic potential on to an isodensity surface. However, the spectrum of colors which HC5 uses as default gives a rather subtle image. Most of the other packages (e.g. Cerius) that have this function use a spectrum from red to blue including the intermediate yellows and greens to give (to me anyway) a more meaningful picture. Is it possible to change the HC color spectrum on this function? Otherwise, I like the new display and rendering options. Steve Rogers ICI Technology Runcorn UK From - Wed May 14 10:38:04 1997 Message-ID: <3379CE4C.467E@hyper.com> Date: Wed, 14 May 1997 10:38:04 -0400 From: Krassimir Stavrev Organization: Hypercube, Inc. X-Mailer: Mozilla 3.0 (Win95; I) MIME-Version: 1.0 To: ACCOMAZZ@ICIL64.CILEA.IT, hyperchem@hyper.com Subject: Re: File conversion utility requested References: <01IITHG6MIJM00726C@ICIL64.CILEA.IT> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mozilla-Status: 0011 Content-Length: 1613 ACCOMAZZ@ICIL64.CILEA.IT wrote: > > Hello > > I'm looking for a file conversion utility from the MSI (BioSym or Insight) > .car / .mdf file format to HyperChem (.hin) file format. > > We have HyperChem running on PC's and MSI (BioSym or Insight) on SGI > Workstations. > The problem is how to quicly exchange data and how to read our structures > archive made of files in .car/mdf format. > The procedure we use now is to read and save .hin and .car/.mdf in MDL .mol > format, which is readable / writable from both Hyperchem / MSI (BioSym). > > The most interesting file conversion program I found on the Internet is > >MOL2MOL -- an easy-to-use file conversion program for the chemist > but it can't read directly .car / .mol files. > > If anyone has any kind of information that can help me please contact me > by email directly at this address: > > accomazz@icil64.cilea.it > > ================================ > Dr. Paolo Accomazzi > EniChem - Centro Ricerche Novara > via Fauser, 4 > 28100 NOVARA > ITALY Paolo, You can use Babel to convert between various formats. It is a freeware downloadable from various places, see for example ftp://joplin.biosci.arizona.edu/pub/Babel: babel-1.6.tar.Z -- Unix sources and Makefile babel16.zip - MS DOS executable; works also in Win95 DOS box It has .car to .hin conversion, and many others. Regards, Krassimir --- Krassimir Stavrev, PhD Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice: 1-352-371-7744/1-800-960-1871 Fax: 1-352-371-3662 From - Wed May 14 10:54:06 1997 Message-ID: <3379D20D.7BCB@hyper.com> Date: Wed, 14 May 1997 10:54:06 -0400 From: Krassimir Stavrev Organization: Hypercube, Inc. X-Mailer: Mozilla 3.0 (Win95; I) MIME-Version: 1.0 To: steve_rogers@ici.co.uk, hyperchem@hyper.com Subject: Re: ESP surfaces in HyperChem 5 References: <0031900002905653000002*@MHS> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mozilla-Status: 0011 Content-Length: 1069 steve_rogers@ici.co.uk wrote: > > Dear Krassimir, Joel ..., > > I am evaluating HyperChem 5 (Windows 95 version). I am very interested in the > mapping of electrostatic potential on to an isodensity surface. However, the > spectrum of colors which HC5 uses as default gives a rather subtle image. Most > of the other packages (e.g. Cerius) that have this function use a spectrum from > red to blue including the intermediate yellows and greens to give (to me > anyway) a more meaningful picture. Is it possible to change the HC color > spectrum on this function? Otherwise, I like the new display and rendering > options. > > Steve Rogers > ICI Technology > Runcorn > UK Steve, Thanks for your comments. You may wish to try File/Preferences/ Isosurface Colors and see which combination of colors suits you best. Regards, Krassimir --- Krassimir Stavrev, PhD Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice: 1-352-371-7744/1-800-960-1871 Fax: 1-352-371-3662 From - Fri May 16 08:04:13 1997 Date: Thu, 15 May 1997 16:22:02 -0700 (MST) From: Paul Calvert To: hyperchem@hyper.com Subject: Painful reminder Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Mozilla-Status: 0001 Content-Length: 324 I would like to pass on a warning to not trust the Hyperchem dongle for data transfer. I forgot it was on my machine when I plugged in my zip drive to the printer cable, mangled 50 MB of data and tried all sorts of fixes until I remembered the dongle and took it out of the line. Paul Calvert University of Arizona From - Fri May 16 08:04:12 1997 From: Joel Polowin To: "'hyperchem@hyper.com'" , "'steve_rogers@ici.co.uk'" Subject: Re: ESP surfaces in HyperChem 5 Date: Thu, 15 May 1997 12:15:00 -0400 Message-Id: <337B3829@office.agissa> X-Mailer: Microsoft Mail V3.0 X-Mozilla-Status: 0011 Content-Length: 1709 steve_rogers@ici.co.uk writes: > > I am evaluating HyperChem 5 (Windows 95 version). I am very interested in the > > mapping of electrostatic potential on to an isodensity surface. However, the > > spectrum of colors which HC5 uses as default gives a rather subtle image. Most > > of the other packages (e.g. Cerius) that have this function use a spectrum from > > red to blue including the intermediate yellows and greens to give (to me > > anyway) a more meaningful picture. Is it possible to change the HC color > > spectrum on this function? Otherwise, I like the new display and rendering > > options. The colour limitation is that the menu allows you to select a "starting colour" and an "ending colour", both of which are defined in terms of whether or not they include each of red, green, and blue. For example, when red and green are "on" but blue is "off", the result is yellow. When all three colours are "off", the result is black; when all are on, the result is white. The "middle colour" that HyperChem draws is the sum of the starting and ending colours; for example, if you have green and purple (red + blue) as your endpoints, the middle colour will be white (red + green + blue). The greatest colour range that you can get with HyperChem is by choosing red and green as the ends; that way you get yellow (red + green) in the middle, and some orange (2/3 red + 1/3 green) between the red and yellow. This even follows the expected spectral pattern. You can get some rather striking effects if you choose one endpoint colour to be the same as the screen background colour, especially if that's black. Joel joelp@agiss.com From - Fri May 16 08:04:14 1997 Message-ID: <337C08DF.2097@ignet.odessa.ua> Date: Fri, 16 May 1997 10:12:31 +0300 From: Yuri Kruglyak Reply-To: quantum@ignet.odessa.ua Organization: QuantumNet X-Mailer: Mozilla 3.0 (Win95; I) MIME-Version: 1.0 To: hyperchem@hyper.com Subject: Change my address References: Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit X-Mozilla-Status: 0001 Content-Length: 1152 Dear HyperChem, I am in HyperChem list. Please, change my address from quantum@ignet.odessa.ua to kruglyak@qnet.odessa.ua Thank you, Yuri Kruglyak ======================================================================= Professor Yuri Kruglyak Department of Molecular Electronics kruglyak@qnet.odessa.ua Odessa State University quantum@ignet.odessa.ua Dvoryanskaya St. 2 FaxLine: +380-482-637785 ODESSA 270100 UKRAINE Voice : +380-482-603314 ======================================================================= QuantumNet Public Association: http://www.ignet.odessa.ua/quantum/qnet.htm [Main office in Odessa] http://www.patriot.net/users/eslone/qnet [QuantumNet U.S. Office] http://ccl.osc.edu/cca/info/societies/qnet/qnet.html [CompuChem List] ======================================================================= Richard P. Feynman' Foundation Friends of Tuva' FSU Office: www.patriot.net/users/eslone/tuva.htm ======================================================================= From - Fri May 16 08:04:11 1997 From: steve_rogers@ici.co.uk X400-Originator: steve_rogers@ici.co.uk X400-Recipients: hyperchem@hyper.com X400-MTS-Identifier: [/PRMD=ICI/ADMD=TMAILUK/C=GB/;0031900002920093000002] X400-Content-Type: P2-1988 (22) Message-ID: <0031900002920093000002*@MHS> To: " - (052)hyperchem (a) hyper.com" Subject: Electrostatic Potential Surfaces, etc in HyperChem Date: Thu, 15 May 1997 09:13:34 +0100 X-Mozilla-Status: 0001 Content-Length: 986 Krassimir, > Thanks for your comments. You may wish to try File/Preferences/ Isosurface Colors and see > which combination of colors suits you best. Many thanks - that helps quite a lot. However, ideally I think a spectrum of colors should be used and not just a gradation between two colors. This enables a much clearer picture of the neutral parts of the molecule. On a similar topic, is it possible to calculate electrostatic potential derived charges using HyperChem? By this I mean partial charges on the atoms centres that are fitted to reporduce the electrostatic potential at an isodensity surface. Routines exist in MOPAC and Gaussian to do this; for example, the CHelpG method of Breneman and Wiberg (J. Comp. Chem., 11, 361, 1990) is implimented in Gaussian. We have found that such charges are almost independent of basis set and give the best representation of intermolecular electrostatic interactions. Steve Rogers ICI Technology Runcorn UK From - Fri May 16 10:23:52 1997 From: jsalb@ix.netcom.com (Jesse Salb) To: Krassimir Stavrev Subject: Re: NT Service Pack 3 and HyperChem Date: Fri, 16 May 1997 13:50:01 GMT Message-ID: <337c6593.29237120@smtp.ix.netcom.com> References: <337bedae.917319@smtp.ix.netcom.com> <337C535A.7548@hyper.com> In-Reply-To: <337C535A.7548@hyper.com> X-Mailer: Forte Agent 1.01/32.397 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mozilla-Status: 0011 Content-Length: 1004 Krassimir, Let me run HC and CP exhaustively over the weekend and I'll email you on Monday. You could put that in the archive. Jesse On Fri, 16 May 1997 08:30:18 -0400, you wrote: >Jesse Salb wrote: >> >> Krassimir, >> >> Service Pack 3 has just been released for NT 4.0 on the Microsoft web >> site. After about 4 hours of testing, I can report that both HC 5.01 >> and CP 1.6 seem to work smoothly with the service pack installed. (The >> previous bugs in these apps are still there, of course). >> >> This is good news, as NT service packs have been known to break apps >> in the past. >> >> Regards, >> Jesse Salb > > >Thank you, Jesse - can I put your e-mail in the newgroup >archive for May so that more people could know about NT? > >Regards, >Krassimir >--- >Krassimir Stavrev, PhD >Hypercube, Inc. Florida Science and Technology Park >1115 N.W. 4th Street Gainesville, Florida 32601 >Voice: 1-352-371-7744/1-800-960-1871 Fax: 1-352-371-3662 > From - Tue May 20 07:48:19 1997 From: steve_rogers@ici.co.uk X400-Originator: steve_rogers@ici.co.uk X400-Recipients: hyperchem@hyper.com X400-MTS-Identifier: [/PRMD=ICI/ADMD=TMAILUK/C=GB/;0031900002947202000002] X400-Content-Type: P2-1988 (22) Message-ID: <0031900002947202000002*@MHS> To: " - (052)hyperchem (a) hyper.com" Subject: Specifying Chain Conformations/Stereochemistry during Buildi Date: Tue, 20 May 1997 10:19:40 +0100 X-Mozilla-Status: 0001 Content-Length: 1241 Hi, I've been trying to build some structures which incorporate oligomeric chains of ethylene oxide, HO-(CH2CH2O)n-H. The lowest energy conformation for these chains is a TTG helix from the crystal structure, the C-C bond being the gauche state. I can set this up by selecting atoms and specifying the bond torsions in the usual way. However, when I come to change the chain length or add a functional group to the end of the chain the command "Build/Add H & Model Build" changes the conformation to all trans again. It is becoming frustrating to have to specify all the bond torsions over again. Is there a way of stopping the build command changing the conformation I've set up in a fragment that I prepared earlier? On a similar topic, I have also been interested in building structures based on glucose and derivatives. The problem I have here is that the build command often changes the stereochemistry. Is there an easy way of converting Fischer or Haworth projections into 3-D structures having the correct stereochemistry? I realise this is a lot to ask of a 2D->3D conversion program and that I probably need a 3D builder. Thanks for your help in advance, Steve Rogers ICI Technology Runcorn UK From - Tue May 20 09:27:27 1997 Message-ID: <3381A6BF.7D96@hyper.com> Date: Tue, 20 May 1997 09:27:27 -0400 From: Krassimir Stavrev Organization: Hypercube, Inc. X-Mailer: Mozilla 3.0 (Win95; I) MIME-Version: 1.0 To: steve_rogers@ici.co.uk, hyperchem@hyper.com Subject: Re: Specifying Chain Conformations/Stereochemistry during Buildi References: <0031900002947202000002*@MHS> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mozilla-Status: 0011 Content-Length: 2507 steve_rogers@ici.co.uk wrote: > > Hi, > > I've been trying to build some structures which incorporate oligomeric chains > of ethylene oxide, HO-(CH2CH2O)n-H. The lowest energy conformation for these > chains is a TTG helix from the crystal structure, the C-C bond being the gauche > state. I can set this up by selecting atoms and specifying the bond torsions > in the usual way. However, when I come to change the chain length or add a > functional group to the end of the chain the command "Build/Add H & Model > Build" changes the conformation to all trans again. It is becoming frustrating > to have to specify all the bond torsions over again. Is there a way of > stopping the build command changing the conformation I've set up in a fragment > that I prepared earlier? Hi Steve, Yes, you can do this by applying constraints from the Build menu. You can apply them manually (bond by bond..), or you may consider writing a script which can set the constraints for you. For more details on how to use constraints, please see your G.S. manual, Lesson 12, as well as the CDK manual, pp. 216-217 for the corresponding script commands. Cis- and trans- constraints can also be set through the Build menu. > On a similar topic, I have also been interested in building structures based on > glucose and derivatives. The problem I have here is that the build command > often changes the stereochemistry. Is there an easy way of converting Fischer > or Haworth projections into 3-D structures having the correct stereochemistry? > I realise this is a lot to ask of a 2D->3D conversion program and that I > probably need a 3D builder. Saccharides can be most easily built by ChemPlus which has a builder specifically designed for that. You can also use, to some extent, the Builder in HyperChem as it evaluates the chirality of the atoms; you can label those R or S from the Labels menu. A good explanation of the 2D->3D conversion capabilities of the Builder is given in the Reference manual, pp. 303-305. Its limitations and abilities to create only approximate structures (which can be further optimized by using quantum or molecular mechanics methods) are also explained in some detail there. Regards, Krassimir --- Krassimir Stavrev, PhD, support@hyper.com Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice: 1-352-371-7744/1-800-960-1871 Fax: 1-352-371-3662 From - Tue May 20 13:37:09 1997 Date: Tue, 20 May 1997 13:32:54 -0400 From: "CYCLOLAB R&D Lab." Subject: Re2: Specifying Chain Conformations/Stereochemistry during Buildi To: Krassimir Stavrev Message-ID: <199705201333_MC2-16FA-5998@compuserve.com> MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline X-Mozilla-Status: 0001 Content-Length: 6503 Hi Krassimir, herewith I'm sendig to you my answer to Steve, perhaps you will find = it useful in the future. Best regards, Laszlo > Hi Steve, As an experienced glucose-oligomer biulder, I can advice you to = eliminate the use of BUILD menu when you've set the sugar manually. I do not why = it has not been corrected but HC usually build stupid molecules when too = much (>2!) stereomeric centre exist. Use IsisDraw for building sugars, if ChemPlus is unmavailable! The = built molecules can be imported directly (otherwise, IsisDraw can handle 3D structures, and free for personal use) and use MM+ with bond dipole = option. It requires several hundrends more cycles but the result is worth. This method can be used when the Builder gives wrong molecules. I had = similar problems with cyclodextrins (1->4 alpha[glcp]6-12) and e.g. taxol derivatives, or in cases of some alkaloids, etc. If you cannot overview = the optical isomeric changes, this method always give satisfactory results. In this letter I'm sending to you the three ab initio optimalized = glucoses for help. Simply cut between **** and create an ASCII file and paste = into that file and save (you must use quotation marks, like "gg.hin" = otherwise you will get a file with two extensions like gg.hin.txt) But! NEVER USE = the BUILD MENU when you have finished the building of your molecule. Regards, Laszlo gg conformer ********** ;Gaussian ab Initio opt. STO-3G* Opt. All atoms have = charge ;HF=3D-683.3338651 ;Dipole=3D2.9 forcefield mm+ sys 0 view 40 0.21018 55 15 1 0 0 0 1 0 0 0 1 0.04 -0.12145 -54.94 mol 1 gg_full atom 1 - O O2 - -0.765872 1.2598 -1.7802 1.1052 2 2 s 23 s atom 2 - C C4 - 0.428485 0.8022 -1.499 -0.1806 4 7 s 3 s 1 s 13 s atom 3 - O O2 - -0.693765 -0.577 -1.3657 -0.2286 2 2 s 4 s atom 4 - C C4 - 0.113402 -1.1588 -0.2918 0.4997 4 5 s 3 s 8 s 14 s atom 5 - C C4 - 0.152134 -0.5578 1.0318 0.0415 4 6 s 4 s 9 s 15 s atom 6 - C C4 - 0.131411 0.9561 0.9758 0.1431 4 7 s 5 s 10 s 16 s atom 7 - C C4 - 0.125953 1.4988 -0.2192 -0.6266 4 2 s 6 s 11 s 17 s atom 8 - C C4 - 0.003187 -2.6549 -0.3916 0.2546 4 4 s 12 s 18 s 19 s atom 9 - O O2 - -0.772159 -1.0774 2.036 0.8651 2 5 s 24 s atom 10 - O O2 - -0.780874 1.4584 2.179 -0.3733 2 6 s 20 s atom 11 - O O2 - -0.775671 2.8896 -0.3168 -0.4967 2 7 s 21 s atom 12 - O O2 - -0.746012 -2.9696 -0.3371 -1.1061 2 8 s 22 s atom 13 - H H - 0.187457 1.0407 -2.3146 -0.8508 1 2 s atom 14 - H H - 0.183994 -0.9628 -0.416 1.5595 1 4 s atom 15 - H H - 0.189042 -0.8337 1.2056 -0.9941 1 5 s atom 16 - H H - 0.172575 1.2277 0.88 1.1921 1 6 s atom 17 - H H - 0.197528 1.2979 -0.072 -1.6802 1 7 s atom 18 - H H - 0.152305 -3.0191 -1.3154 0.6984 1 8 s atom 19 - H H - 0.203183 -3.1534 0.4381 0.7331 1 8 s atom 20 - H HO - 0.459662 2.4058 2.1282 -0.3987 1 10 s atom 21 - H HO - 0.462398 3.0841 -0.69 0.3551 1 11 s atom 22 - H HO - 0.450484 -2.5135 -1.0445 -1.5427 1 12 s atom 23 - H HO - 0.457941 0.9169 -2.6169 1.3918 1 1 s atom 24 - H HO - 0.463212 -0.6748 2.8598 0.621 1 9 s endmol 1 ********** gt conformer ********** ;Gaussian ab Initio opt. STO-3G* Opt. All atoms have charge ;HF=3D-683.3292216 ;Dipole=3D1.4 forcefield mm+ sys 0 view 40 0.20427 55 15 1 0 0 0 1 0 0 0 1 0.30805 -0.1499 -54.843 mol 1 gt_full atom 1 - O O2 - -0.770608 0.691 -1.9618 1.0161 2 2 s 23 s atom 2 - C C4 - 0.426537 0.5652 -1.5463 -0.3096 4 7 s 3 s 1 s 13 s atom 3 - O O2 - -0.66128 -0.7117 -1.1043 -0.6055 2 2 s 4 s atom 4 - C C4 - 0.125353 -1.1809 0.0349 0.0899 4 5 s 3 s 8 s 14 s atom 5 - C C4 - 0.143746 -0.2464 1.2106 -0.1767 4 6 s 4 s 9 s 15 s atom 6 - C C4 - 0.128651 1.1732 0.8249 0.1992 4 7 s 5 s 10 s 16 s atom 7 - C C4 - 0.126778 1.5958 -0.4442 -0.5258 4 2 s 6 s 11 s 17 s atom 8 - C C4 - 0.006765 -2.6022 0.2938 -0.3812 4 4 s 12 s 18 s 19 s atom 9 - O O2 - -0.772729 -0.6846 2.3026 0.5802 2 5 s 24 s atom 10 - O O2 - -0.783089 2.0054 1.9034 -0.1354 2 6 s 20 s atom 11 - O O2 - -0.777291 2.8788 -0.8435 -0.1315 2 7 s 21 s atom 12 - O O2 - -0.740499 -3.4949 -0.6988 0.0445 2 8 s 22 s atom 13 - H H - 0.189745 0.7499 -2.3747 -0.9806 1 2 s atom 14 - H H - 0.171692 -1.189 -0.1623 1.1578 1 4 s atom 15 - H H - 0.16869 -0.2691 1.4504 -1.2388 1 5 s atom 16 - H H - 0.173555 1.206 0.6512 1.2725 1 6 s atom 17 - H H - 0.197073 1.6501 -0.2342 -1.5864 1 7 s atom 18 - H H - 0.181482 -2.9155 1.2754 -0.0439 1 8 s atom 19 - H H - 0.179856 -2.6197 0.2816 -1.4627 1 8 s atom 20 - H HO - 0.461274 2.9078 1.6484 0.0126 1 10 s atom 21 - H HO - 0.463479 2.8078 -1.2916 0.7032 1 11 s atom 22 - H HO - 0.43582 -3.6984 -0.5663 0.9597 1 12 s atom 23 - H HO - 0.459845 0.1057 -2.6918 1.1743 1 1 s atom 24 - H HO - 0.465156 -0.0354 2.9916 0.5102 1 9 s endmol 1 ********* tg conformer ********* ;Gaussian ab Initio opt. STO-3G* Opt. All atoms have charge ;HF=3D-683.3340479 ;Dipole=3D2.2 forcefield mm+ sys 0 view 40 0.21489 55 15 1 0 0 0 1 0 0 0 1 0.21805 -0.0036 -54.859 mol 1 tg_full atom 1 - O O2 - -0.766959 1.3154 -1.7705 1.0437 2 2 s 23 s atom 2 - C C4 - 0.425279 1.0972 -1.4309 -0.2902 4 7 s 3 s 1 s 13 s atom 3 - O O2 - -0.67678 -0.2475 -1.4503 -0.6257 2 2 s 4 s atom 4 - C C4 - 0.110356 -1.0897 -0.5313 0.0473 4 5 s 3 s 8 s 14 s atom 5 - C C4 - 0.153274 -0.5917 0.8811 -0.2428 4 6 s 4 s 9 s 15 s atom 6 - C C4 - 0.128936 0.854 1.0142 0.1951 4 7 s 5 s 10 s 16 s atom 7 - C C4 - 0.127507 1.7034 -0.0457 -0.4929 4 2 s 6 s 11 s 17 s atom 8 - C C4 - 0.021491 -2.5071 -0.7909 -0.4505 4 4 s 12 s 18 s 19 s atom 9 - O O2 - -0.790783 -1.4141 1.7977 0.4284 2 5 s 24 s atom 10 - O O2 - -0.783502 1.2797 2.3066 -0.1445 2 6 s 20 s atom 11 - O O2 - -0.7762 3.0314 0.0096 -0.0548 2 7 s 21 s atom 12 - O O2 - -0.763948 -3.4675 -0.1668 0.3452 2 8 s 22 s atom 13 - H H - 0.190303 1.5711 -2.1507 -0.9444 1 2 s atom 14 - H H - 0.194237 -1.0629 -0.71 1.1161 1 4 s atom 15 - H H - 0.171688 -0.6428 1.0532 -1.3164 1 5 s atom 16 - H H - 0.17749 0.9057 0.8767 1.2726 1 6 s atom 17 - H H - 0.1979 1.72 0.1655 -1.5545 1 7 s atom 18 - H H - 0.14535 -2.5879 -0.4881 -1.493 1 8 s atom 19 - H H - 0.180605 -2.6965 -1.8546 -0.4028 1 8 s atom 20 - H HO - 0.462232 2.2077 2.3819 0.0404 1 10 s atom 21 - H HO - 0.464251 3.0866 -0.4265 0.7875 1 11 s atom 22 - H HO - 0.475959 -3.2566 0.7558 0.4194 1 12 s atom 23 - H HO - 0.45978 1.0152 -2.6565 1.2021 1 1 s atom 24 - H HO - 0.471532 -1.0345 2.6637 0.3397 1 9 s endmol 1 ******* From - Wed May 28 10:48:34 1997 Received: from MAILQUEUE by VIRGIL (Mercury 1.21); 27 May 97 11:58:31 +0100 From: "MORTEN LANGGaaRD - BIOKEM" Organization: Roskilde Universitetscenter To: Krassimir Stavrev Date: Tue, 27 May 1997 11:58:31 +0100 Subject: Re: Specifying Chain Conformations/Stereochemistry during B Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <48BD006311@virgil.ruc.dk> X-Mozilla-Status: 0011 Content-Length: 2221 Dear Krassimir, I tried to send the following message to Hyperchem@hyper.com but I got this message back from the mail delivery subsystem: The original message was received at Thu, 22 May 1997 11:19:40 +0200 (MET DST) from virgil.ruc.dk [130.225.220.110] ----- The following addresses had permanent fatal errors ----- ----- Transcript of session follows ----- 451 ... hyper.com: Name server timeout Message could not be delivered for 5 days Message will be deleted from queue Do you have a problem? Here is my original posting: Just a simple remark to Steve's question about the modelbuilder. I guess that Krassimir's suggestion about applying constraints is the in general most correct answer. Nevertheless is occur to me that Steve's problem might be solved in a somewhat less tedious manner. I would like to draw your attention to the fact that the modelbuilder only works on selected part of a molecule. For example, to change or modify only a part of a molecule (e.g. convert a methyl group into a benzyl group) you simply add/draw the lacking atoms in the usual way. Now, it is possible to restrict the modelbuilder to work only on the "new part" by limiting the selection to the new atoms. Maybe this answer is too simple - but I don't know how well known this "unknown" feature actually is :). I had used HyperChem for a long time before I discovered this nice trick. I don't think it is describe anywhere in the manuals. Best regards Morten =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Morten Langgaard Department of Chemistry Phone: +45 46757781 * 2471 Roskilde University (RUC) Fax: +45 46757721 POB 260, DK-4000 Roskilde, Denmark E-Mail: ml@virgil.ruc.dk =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From - Wed May 28 13:07:20 1997 From: jsalb@ix.netcom.com (Jesse Salb) To: hyperchem@hyper.com Subject: HyperChem 5.01 w/ Nt 4.0 and SP3 Date: Tue, 27 May 1997 17:53:07 GMT Message-ID: <338b1f5f.49461912@smtp.ix.netcom.com> X-Mailer: Forte Agent 1.01/32.397 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mozilla-Status: 0001 Content-Length: 292 After extensive testing of HyperChem 5.01c and ChemPlus 1.6 on NT 4.0 with the newly released Service Pack 3, I can report that this combination of apps works smoothly with no new bugs introduced. The original bugs in HyperChem and ChemPlus still remain, of course (hint). Jesse Salb From - Wed May 28 13:14:48 1997 From: Joel Polowin To: "'hyperchem@hyper.com'" Subject: Re: Specifying Chain Conformations/Stereochemistry during Buildi Date: Tue, 27 May 1997 17:59:00 -0400 Message-Id: <338CAB99@office.agissa> X-Mailer: Microsoft Mail V3.0 X-Mozilla-Status: 0011 Content-Length: 818 Steve Rogers writes: > However, when I come to change the chain length or add a > functional group to the end of the chain the command "Build/Add H & > Model > Build" changes the conformation to all trans again. It is becoming > frustrating > to have to specify all the bond torsions over again. Is there a way of > stopping the build command changing the conformation I've set up in a > fragment that I prepared earlier? Just make sure that only the new atoms are selected before you do the model-building, and only the selected atoms will be moved around. The rest of the chain will not be altered. If you have set up the original structure as a named selection, then you can easily select it by name, and then use Select/Complement to select everything else instead. Joel joelp@agiss.com