From autodesk!sws.mps.ohio-state.EDU!matt@netcom.com Thu Apr 1 23:05:00 1993 Date: Thu, 1 Apr 93 13:49:18 -0400 From: Matthew Lynn Subject: Aligning internal axes To: hyperchem@autodesk.com Status: RO I have an inorganic molecule whose geometry is trigonal bipyramidal and I have drawn it in HyperChem. My problem is that I would like to place the central metal at the origin (which I have done) and align the x-axis of the metal atom along a metal atom-equatorial atom bond and the y-axis along a metal atom-axial atom bond. Is this possible? Thanks for your help. Matt ________________________________________________________________________ From hyper!slee@autodesk.com Fri Apr 2 00:14:46 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: Aligning internal axes To: autodesk!hyperchem@netcom.com Date: Thu, 1 Apr 93 16:42:36 EST Status: RO > > I have an inorganic molecule whose geometry is trigonal bipyramidal and > I have drawn it in HyperChem. My problem is that I would like to place > the central metal at the origin (which I have done) and align the x-axis of > the metal atom along a metal atom-equatorial atom bond and the y-axis > along a metal atom-axial atom bond. Is this possible? Thanks for your > help. > Matt > The Align Molecules item under the Edit menu allows you to align inertial axes of the system with selected axes of the molecular coordinate system. If you have selected a part of the molecule then the inertial axes refer to the selection, not to the whole molecule, and this enables you to do what you want. You can check their direction by turning on Display Inertial Axes item. If you select a bond (eg, metal-eq. atom) then the primary inertial axis points along the bond, and you can align this with the molecular coordinate system axis of choice. You may need to retranslate the metal atom to the origin after these realignments. Tom -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From uoft02.utoledo.edu!DSMITH@netcom.com Fri Apr 2 11:15:41 1993 Date: Fri, 02 Apr 1993 10:30:18 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: call for Posters - Chicago To: chemistry@osc.edu, mmodinfo@uoft02.utoledo.edu, hyperchem@autodesk.com Status: RO The Computers in Chemistry Division of the ACS is sponsoring a symposium entitled "Modeling the Hydrogen Bond" which will run for two full days at the Chicago meeting in August (22nd - 27th). We have approximately 25 speakers, and the sessions will be set up along the general lines of Methodology, Organic, and Biochemistry. We are now soliciting posters for this symposium. Posters may be put into a special session, the general division poster session, or possibly Sci-Mix. Submissions by graduate students are especially solicited. In fact, up to 10 graduate students will be eligible for reimbursement of travel and associated costs up to $300. To submit: Please send one (1) copy of your abstract on the standard ACS abstract form to me at the address listed below by April 25th, 1993. Faxed submissions are acceptible ONLY if an original is also sent in time to meet the deadline. Graduate students: If you wish to apply for travel funds, please attach a separate letter to your abstract with a short justification why you should receive the funds. We are looking forward to a great symposium. I hope to see you all there! Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu ________________________________________________________________________ From hyper!slee@autodesk.com Fri Apr 2 19:27:50 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: HyperChem Release 3 To: autodesk!hyperchem@netcom.com (HyperChem e-mail group) Date: Fri, 2 Apr 93 16:42:19 EST Status: RO RELEASE 3 OF HYPERCHEM FOR WINDOWS ================================== Waterloo, Ontario -- March 29, 1993 Hypercube has now completed HyperChem(TM) Release 3 for Windows(TM). HyperChem is developed by Hypercube, and is licensed to Autodesk(R), Inc., who have announced that it will be available in April. Release 3 is a major upgrade of HyperChem. HyperChem Release 2, introduced one year ago, created a new standard for molecular modeling on the PC, by bringing extensive molecular modeling capabilities to the Windows operating environment. HyperChem now has the largest installed base of PC molecular simulation software. It is used for teaching and research in over 400 colleges and universities. Major New Features ------------------ o Easy and complete control over stereochemistry. o Computation, display and analysis of IR and UV spectra from semi-empirical methods, with static and dynamic display of vibrational normal modes. o Additional file and clipboard formats supported. o Ribbons display of peptides and proteins. o Up to twelve bonded neighbours handled by model builder and by all computational methods. o Improved semi-empirical quantum mechanics computations: - Several-fold speed increase. - INDO/1 and INDO/S methods included for transition metals. - PM3 method added. - Computation of part of a system available for all methods. - User-specified restraining forces to constrain geometries. - Interactive energy-level diagram for choosing and inspecting molecular orbitals. o Control of initial velocities for dynamics calculations from the user interface. o Faster and more extensive script and Windows DDE capabilities, including: - MO coefficients and energies. - Grids of computed electronic properties. - Spectroscopic transitions and normal modes. HyperChem Release 3 has the untapped potential to run remote calculations on UNIX computers. This will require a third party implementation of the new Windows WINSOCK protocol and not-yet-available versions of the computational modules installed on the UNIX computer. Pricing and Availability ------------------------ HyperChem is licensed to Autodesk, Inc., who should be contacted for information about pricing and availability. Hypercube Inc. -------------- Hypercube develops scientific software, with particular expertise in parallel processing, and also provides consulting services in molecular modeling. It is located in Waterloo, Ontario, Canada. For more information about Hypercube's services, including custom software and scientific support contracts for HyperChem, contact your Authorized HyperChem Dealer. Hypercube can be reached by phone at 519-725-4040, fax at 519-725-5193, and on Internet at info@hyper.com. --------- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From cw-f1.umd.umich.edu!RPOTTS@netcom.com Mon Apr 5 12:43:01 1993 To: hyperchem@autodesk.com From: "professor potts" Organization: University of Michigan-Dearborn Date: 5 Apr 93 09:24:26 EST5EDT Subject: Question Status: RO How do you capture the status line (bond distances and angles) to the log file? ________________________________________________________________________ From hyper!slee@autodesk.com Mon Apr 5 15:11:37 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: Question To: autodesk!hyperchem@netcom.com (HyperChem e-mail group) Date: Mon, 5 Apr 93 14:14:45 EDT Status: RO > > How do you capture the status line (bond distances and angles) to the > log file? > The best way to do this is by scripts if you are interested in specific distances and angles. If you want all the bond lengths and angles at once, by the way, you can force it by doing an MM+ single point calculation with PrintLevel set to 1. The script variable "status-message" returns a string with the most recent status-line message, as what we call an "omsg", or output message. To direct the omsg's to a file you use the script command "omsgs-to-file filename" (which replaces the file "filename") or "append-omsgs-to-file filename" (which obviously sticks the omsgs at the end of the file). The status-line is a very transient thing, so you will want to produce the status-line within the script (otherwise it is over-written when you open a script file). So you could do something like the following script. All lines beginning with semi-colons are treated by HyperChem as comment lines. ;================================================================= ; Decide where to send the messages append-omsgs-to-file temp.txt ; Make sure that selecting the atoms gives what you want selection-target atoms multiple-selections yes ; Remove "status-message =" from the response query-response-has-tag No ; Select atoms 1 and 2 in molecule 1 select-atom 1,1 select-atom 2,1 ; Query the status message ; (This line could also be "query-value status-message") status-message ? ;================================================================= Hope this helps. If you haven't used scripts before, I think you will find it surprisingly easy. Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From hyper!slee@autodesk.com Mon Apr 5 17:48:01 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Status-message to file: oops! To: autodesk!hyperchem@netcom.com (HyperChem e-mail group) Date: Mon, 5 Apr 93 16:46:43 EDT Status: RO A recent query to the list asked: > How do you capture the status line (bond distances and angles) to the > log file? ...and I answered with a description of a script that would produce this information. Unfortunately, I was working with Release 3 when I tested my response. I later checked with Release 2, and found that the "status-message" command was not implemented as a variable in Release 2.0, simply as a command. Therefore, it can be set but not queried, and the script does not work. The MM+ single point route I mentioned in my previous post is probably the best way to get bond angle and bond distance information into a file in Release 2. Now, I know this sounds like a plug for the next release, but that is not how it was intended (honest)! However, having already started, I should point out that a neater solution in a few weeks is to use a script command that queries the value of the current selection, and send that to a file, rather than go by the status line. My apologies to anybody trying to get my script to work on their current copy of HyperChem. Tom Slee ________________________________________________________________________ From uoft02.utoledo.edu!DSMITH@netcom.com Tue Apr 13 10:50:41 1993 Date: Tue, 13 Apr 1993 10:07:59 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: stereo viewing in molecular modeling To: chemistry@osc.edu, hyperchem@autodesk.com, mmodinfo@uoft02.utoledo.edu Status: RO I have a general question for anyone out there who wishing to open a dialog about stereo viewing for molecular modeling. Please send responses directly to me and I will summarize for the net. Most graphical user interfaces have provided a limited version of stereo viewing capability for years. This typically involves presenting a right and left eye view on screen, where one view is rotated slightly with respect to the first. Three dimensional viewing required the user to cross his/her eyes and focus the two images one on top of the other. With high resolution monitors using refresh rates of 120 Hz, stereoscopic images are produced by rendering alternating left and right images on the screen (i.e. each appears 60 times per second) while the user wears special glasses. The technology has advanced to the point where it is no longer uncomfortable to wear or use the glasses. The image seen now has true perspective and dimension in the z direction (into the screen). Is this type of three-dimensional viewing of use in molecular modeling, or is the current use of shading, etc. to generate flat 2D representations of 3D objects sufficient? Note that even with the stereo glasses, as one moves relative to the screen, i.e. changes the direction of viewing from straight on to side on, one still never sees any additional portions of the image which were previously hidden. That requires moving the object on the screen. In addition to opinions, I would like to hear success stories where the use of 3D viewing has enhanced the chemistry or helped to solve a problem which was insoluble without it or would have taken a longer time or would have resulted in a lower quality answer. Finally, thoughts on virtual reality for molecular modeling are solicited as well. Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu ________________________________________________________________________ From uoft02.utoledo.edu!DSMITH@netcom.com Wed Apr 14 13:07:29 1993 Date: Wed, 14 Apr 1993 12:31:59 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: second call for posters To: chemistry@osc.edu, mmodinfo@uoft02.utoledo.edu, hyperchem@autodesk.com Status: RO SECOND CALL: (Note that some money for graduate students is still available.) The Computers in Chemistry Division of the ACS is sponsoring a symposium entitled "Modeling the Hydrogen Bond" which will run for two full days at the Chicago meeting in August (22nd - 27th). We have approximately 25 speakers, and the sessions will be set up along the general lines of Methodology, Organic, and Biochemistry. We are now soliciting posters for this symposium. Posters may be put into a special session, the general division poster session, or possibly Sci-Mix. Submissions by graduate students are especially solicited. In fact, up to 10 graduate students will be eligible for reimbursement of travel and associated costs up to $300. To submit: Please send one (1) copy of your abstract on the standard ACS abstract form to me at the address listed below by April 25th, 1993. Faxed submissions are acceptible ONLY if an original is also sent in time to meet the deadline. Graduate students: If you wish to apply for travel funds, please attach a separate letter to your abstract with a short justification why you should receive the funds. We are looking forward to a great symposium. I hope to see you all there! Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu ________________________________________________________________________ From hyper!slee@autodesk.com Fri Apr 16 10:38:08 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Script for saving IR spectra To: autodesk!hyperchem@netcom.com (HyperChem e-mail group) Date: Fri, 16 Apr 93 10:27:35 EDT Status: RO Dear HyperChemists, For those of you who upgrade to Release 3, the following scripts may prove useful. They save an IR and UV spectrum so that you can regenerate them at a later date without repeating the computation. Enjoy, Tom Slee ===========================saveir.scr======================================= ; saveir.scr ;=========== ; Save the existing IR spectrum. This script ; produces or writes over the file "\hyper\chem_ir.scr" ; which can be run later to recover the IR data. ; ; When running chem_ir.scr to regenerate the spectrum ; you must first have the appropriate molecule on the screen. ;Direct properly formatted results to the appropriate file query-response-has-tag true omsgs-to-file \hyper\chem_ir.scr status-message "Saving IR spectrum to \hyper\chem_ir.scr" ;Save computational procedure used. calculation-method ? semi-empirical-method ? ;Save semi-empirical options. quantum-total-charge ? multiplicity ? scf-convergene ? max-iterations ? accelerate-scf-convergence ? uhf ? excited-state ? ;Save spectrum ir-band-count ? ir-frequency ? ir-intensity ? ir-intensity-components ? ir-normal-mode ? vibrational-mode ? status-message "Spectrum saved" ===========================saveuv.scr======================================= ; saveuv.scr ;=========== ; Save the existing UV spectrum info. This script ; produces or writes over the file "\hyper\chem_uv.scr" ; which can be run later to recover the UV data. ; ; When running chem_uv.scr you must have the ; appropriate molecule on the screen. ; ;Direct properly formatted results to the appropriate file query-response-has-tag true omsgs-to-file \hyper\chem_uv.scr status-message "Saving UV spectrum to \hyper\chem_uv.scr" ;Save computational procedure used. calculation-method ? semi-empirical-method ? ;Save semi-empirical options. quantum-total-charge ? multiplicity ? scf-convergence ? max-iterations ? accelerate-scf-convergence ? uhf ? excited-state ? zindo-1-sigma-sigma ? zindo-1-pi-pi ? zindo-s-sigma-sigma ? zindo-s-pi-pi ? configuration-interaction ? ;Save CI options. ci-criterion ? ci-occupied-orbitals ? ci-unoccupied-orbitals ? ci-excitation-energy ? ;Save spectrum uv-band-count ? uv-energy ? uv-spin ? uv-total-dipole ? uv-dipole-components ? uv-oscillator-strength ? uv-transition-dipole ? status-message "Spectrum saved" -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From hyper!slee@autodesk.com Thu Apr 22 19:27:25 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: Molecular Volumes To: autodesk!hyperchem@netcom.com (HyperChem e-mail group) Date: Thu, 22 Apr 93 17:00:47 EDT Status: RO Message sent to hyperchem-request: forwarded to the list. --------------------------------------------------------------------------- David writes: | | I have HyperChem 2.0 and Visual Basic 1.0, and I need help with the coding | to select atoms in HyperChem using DDE from Visual Basic. I need to link | VB to HChem so that the users of the VB file can enter atom numbers, select | the atoms, and get the distance between the selected atoms. I hope to use | this distance as the diameter for the calculation of molecular volume using | a sphere formula. I also need code for doing the same thing for another set | of atoms, so I can use the first set of atom distance as diameter and the | second set of atom distance as height for the use in the cylinder formula. | I would greatly appreciate any help with this task, being that I don't have | much experience with coding with VB. I can send you the file if you need to | look at it. Thanks for your consideration. | To allow the user to select atoms in HyperChem from a Visual Basic program, you need code like the following: 1. Set up a DDE link between a Visual Basic control (of your choice, I'll call it "Control") and HyperChem, following the example in the HyperChem "Getting Started" manual (Lesson 15). 2. Use the command Control.LinkExecute SendString$ where SendString$ is a text string reading something like the following: to select atom 4 in molecule 1, SendString$ = "[select-atom 4,1]" if you have an integer variable Var% that is the number of the atom, then you can construct your string as something like: SendString$ = "[select-atom " + Str$(Var%) + ",1]" where the + signs concatenate strings. You can take your variable from the user, as input to a text box, for example. The syntax for most script commands is the same. Everything has to be put into a single string that is sent to HyperChem by the LinkExecute command. If you want to send two commands at once, you can use a string like: SendString$ = "[command 1][command 2]" Hope this helps, Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040