From jornsm@hal.hahnemann.edu Wed Dec 1 13:54:20 1993 Date: Wed, 01 Dec 1993 13:20:43 EST To: hyperchem@autodesk.com Subject: Transforming a PDB file I'm a new user of Hyperchem. I retrieved a PDB file for a homodimeric protein. The file contains coordinates for one subunit. The file also contains the following message: "The second subunit can be generated from the one presented in this entry by the following transformation XPRIME = 163.6994 - X YPRIME = 72.2018 - Y ZPRIME = Z Can I do this transformation using Hyperchem? I would like to create a file that will enable me to display and explore the homodimeric structure. ________________________________________________________________________ From apa@pop.cc.adfa.oz.au Tue Dec 7 23:14:15 1993 Date: Wed, 8 Dec 1993 14:08:43 +1100 To: hyperchem@autodesk.com From: apa@pop.cc.adfa.oz.au (Alan Arnold) Subject: Hyperchem3 under OS/2 2.1. How? How do you run Hyperchem3 under Win-OS/2? We recently installed OS/2 2.1 on our 486DX2's that have Hyperchem installed and which previously ran under Windows 3.1. I'm new to OS/2 and I assumed (optimistically) that one could 'migrate' HC to Win-OS/2. When I tried this, the HC icon appears as a Win-OS/2 application but when I try to run it, I get the message "Hyperchem must be run under Windows Enhanced Mode". I suspect that I may need to tweak some variable/s that seem to be stored in OS2/install/database.txt. All suggestions gratefully received.... ---- Alan Arnold | e-mail: apa@pop.cc.adfa.oz.au Chem. Department,University College | voice : +61 6 268 8080 Australian Defence Force Academy | fax : +61 6 268 8002 CANBERRA ACT 2601 Australia | ________________________________________________________________________ From apa@pop.cc.adfa.oz.au Thu Dec 9 03:37:31 1993 Date: Thu, 9 Dec 1993 15:50:00 +1100 To: autodesk!hyperchem@openlink.openlink.com From: apa@pop.cc.adfa.oz.au (Alan Arnold) Subject: Hyperchem3 under OS/2 2.1 How??? How do you run Hyperchem3 under Win-OS/2? We recently installed OS/2 2.1 on our 486DX2's that have Hyperchem installed and which previously ran under Windows 3.1. I'm new to OS/2 and I assumed (optimistically) that one could 'migrate' HC to Win-OS/2. When I tried this, the HC icon appears as a Win-OS/2 application but when I try to run it, I get the message "Hyperchem must be run under Windows Enhanced Mode". I suspect that I may need to tweak some variable/s that seem to be stored in OS2/install/database.txt. All suggestions gratefully received.... ---- Alan Arnold | e-mail: apa@pop.cc.adfa.oz.au Chem. Department,University College | voice : +61 6 268 8080 Australian Defence Force Academy | fax : +61 6 268 8002 CANBERRA ACT 2601 Australia | ________________________________________________________________________ From hyper!slee@autodesk.com Thu Dec 9 11:16:31 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Hypercube announces ChemPlus. To: autodesk!hyperchem@openlink.openlink.com (HyperChem e-mail group) Date: Thu, 9 Dec 93 10:41:34 EST Waterloo, December 8, 1993 Hypercube is pleased to announce the release of ChemPlus, a set of extensions for HyperChem. ChemPlus requires HyperChem Release 3 for Windows, and has an introductory price of $395 US. ChemPlus brings many new capabilities to HyperChem users. Some of the major features include high-quality ball-and-stick images, 3D renderings of molecular orbitals, conformational searching, evaluation of Log P, of surface areas and of other indicators, automated building of sugars and crystals, amino acid sequence editing, and RMS overlay. ChemPlus is closely integrated with HyperChem: it adds the individual modules into the HyperChem menus for easy access and all programs use Dynamic Data Exchange for smooth communication with HyperChem. For more information, including a detailed description of ChemPlus's features, contact us on Internet at info@hyper.com. Hypercube, Inc. 419 Phillip Street, Waterloo, Ontario, N2L 3X2. Phone: (519) 725-4040 FAX: (519) 725-5193 ________________________________________________________________________ From hyper!slee@autodesk.com Thu Dec 9 19:44:35 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: Transforming a PDB file To: autodesk!hyperchem@openlink.openlink.com (HyperChem e-mail group) Date: Thu, 9 Dec 93 16:26:08 EST A recent poster wrote: | | I'm a new user of Hyperchem. I retrieved a PDB file for a homodimeric | protein. The file contains coordinates for one subunit. The file also | contains the following message: "The second subunit can be generated from | the one presented in this entry by the following transformation | XPRIME = 163.6994 - X | YPRIME = 72.2018 - Y | ZPRIME = Z | Can I do this transformation using Hyperchem? I would like to create a | file that will enable me to display and explore the homodimeric structure. There is not a straighforward way (which is why noreply until now), but in HyperChem you can do reflections in a plane, as long as the plane is a named selection of at least three atoms called PLANE. Here is a script that enables you to do a transformation of the coordinates of a single molecule to from (x, y, z) to (-x, -y, z) by carrying out two reflections. The final translation required would be better done manually as there is no script command for "translate selection by", just "translate selection to". I hope the script makes sense (or at least the comments, which are on lines starting with semi colons. This script works only on R3. The coordinates ? lines are purely to display the coordinates: you don't really need them. The "create-atom" instructions draw an atom at the origin -- in this case hydrogen atoms (atomic number 1). Tom ----------------------------------------------------------------- ; CHANGEXY.SCR ; Script to transform coordinates from x,y,z to-x, -y, z. ; Requirements: ; - one molecule on the HyperChem screen. ; - run this script. ; The strategy of this script is to set up three artificial atoms ; as a plane,and use the fact that in HyperChem you can reflect ; a selection in a plane to transform the molecule's coordinates by ; reflecting in this "mirror". ;===================================================================== ; get initial coordinates of the molecule, for information. coordinates ? ; setup the PLANE to be used as a mirror create-atom 1 create-atom 1 create-atom 1 multiple-selections yes selection-target molecules select-atom 1,2 select-atom 1,3 select-atom 1,4 name-selection PLANE select-none ; move the PLANE to form a mirror in the YZ plane ; atom 1 in molecule 2 is alread at the origin. select-atom 1,3 translate-selection 0,1,0 select-none select-atom 1,4 translate-selection 0,0,1 select-none ; reflect the molecule of interest in the plane select-atom 1,1 menu-edit-reflect select-none ; move the PLANE to form a mirror in the XZ plane select-atom 1,3 translate-selection 1,0,0 select-none ; reflect the molecule of interest in the plane select-atom 1,1 menu-edit-reflect select-none ; delete the atoms used to create the mirror as we no longer need them. delete-atom 1,4 delete-atom 1,3 delete-atom 1,2 ; centre the molecule in the display menu-display-scale-to-fit -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From uscience@CERF.NET Fri Dec 10 17:45:41 1993 Date: Fri, 10 Dec 1993 13:40:50 -0800 (PST) From: "U.S. Science" Subject: Amber settings To: Hyperchem Autodesk Does anyone know if there is additional reference work done with parameter files for Amber that include any additional organics? (That is since release 3.0) Also, has anyone taken the parameter files from Windows3.0 to upgrade the files in the SGI release.? Thanks in advance Jack Breithart uscience@cerf.net 619-523-1949 ________________________________________________________________________ From hyper!hurst@autodesk.com Mon Dec 13 14:03:59 1993 Date: Mon, 13 Dec 93 11:42:43 -0500 From: hyper!hurst@autodesk.com (Graham Hurst) To: autodesk!hyperchem@openlink.openlink.com (HyperChem e-mail group) Subject: Re: Transforming a PDB file Tom Slee wrote: > A recent poster wrote: > | > | I'm a new user of Hyperchem. I retrieved a PDB file for a homodimeric > | protein. The file contains coordinates for one subunit. The file also > | contains the following message: "The second subunit can be generated from > | the one presented in this entry by the following transformation > | XPRIME = 163.6994 - X > | YPRIME = 72.2018 - Y > | ZPRIME = Z > | Can I do this transformation using Hyperchem? I would like to create a > | file that will enable me to display and explore the homodimeric structure. > > There is not a straighforward way (which is why noreply until now), > but in HyperChem you can do reflections in a plane, as long as the > plane is a named selection of at least three atoms called PLANE. > > Here is a script that enables you to do a transformation of the > coordinates of a single molecule to from (x, y, z) to (-x, -y, z) > by carrying out two reflections. The final translation required > would be better done manually as there is no script command for > "translate selection by", just "translate selection to". While Tom is right about no "translate by", in this case you can define reflection planes to perform the translation as well. E.g. first reflect through a plane at X = 163.6994/2 and next reflect through a plane at Y = 72.2018/2. This will do the full transformation that you desire. > I hope the script makes sense (or at least the comments, which are on > lines starting with semi colons). This script works only on R3. > > The coordinates ? lines are purely to display the coordinates: you > don't really need them. > > The "create-atom" instructions draw an atom at the origin -- in this > case hydrogen atoms (atomic number 1). > > Tom Here's a modified version of Tom's script (note that it relies on one and only one molecule being present in HyperChem): -----------cut here---------------------------------------------- ; CHANGEXY.SCR ; Script to transform coordinates from x,y,z to-x, -y, z. ; Requirements: ; - one molecule on the HyperChem screen. ; - run this script. ; The strategy of this script is to set up three artificial atoms ; as a plane,and use the fact that in HyperChem you can reflect ; a selection in a plane to transform the molecule's coordinates by ; reflecting in this "mirror". ;===================================================================== ; get initial coordinates of the molecule, for information. coordinates ? ; setup the PLANE to be used as a mirror create-atom 1 create-atom 1 create-atom 1 multiple-selections yes selection-target molecules select-atom 1,2 select-atom 1,3 select-atom 1,4 name-selection PLANE select-none ; move the PLANE to form a mirror in the YZ plane ; at X = 163.6994/2 select-atom 1,2 translate-selection 68.3497,0,0 select-none select-atom 1,3 translate-selection 68.3497,1,0 select-none select-atom 1,4 translate-selection 68.3497,0,1 select-none ; reflect the molecule of interest in the plane select-atom 1,1 menu-edit-reflect select-none ; move the PLANE to form a mirror in the XZ plane ; at Y = 72.2018/2 select-atom 1,2 translate-selection 0,36.1009,0 select-none select-atom 1,3 translate-selection 1,36.1009,0 select-none select-atom 1,4 translate-selection 0,36.1009,1 select-none ; reflect the molecule of interest in the plane select-atom 1,1 menu-edit-reflect select-none ; delete the atoms used to create the mirror as we no longer need them. delete-atom 1,4 delete-atom 1,3 delete-atom 1,2 ; centre the molecule in the display menu-display-scale-to-fit -----------cut here---------------------------------------------- ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com ________________________________________________________________________ From kellogg@uidaho.edu Wed Dec 29 19:20:45 1993 Date: Wed, 29 Dec 1993 15:10:54 -0700 (PDT) From: Scott Kellogg Subject: ChemPlus Module To: Hyperchem We have recently purchased the ChemPlus module and are having problems with the Sugar Builder. The manual states that a file USER.BTN will exist and yet no such file exists on the hard disk or on the original floppies. We are trying to create our own monosaccharide residues and would like those buttons to be active. Also, is the Help feature under Sugar Builder limited to Version information or should there be more extensive help? The ReadMe file does not help either. ========================================= Scott T. Kellogg Dept. of Microbiol., Mol. Biol. & Biochem. Univ. of Idaho Moscow, ID 83843 Internet: kellogg@crow.csrv.uidaho.edu Phone: 208-885-6966 Fax: 208-885-6518 ________________________________________________________________________ From ujordis@e154jos2.tuwien.ac.at Thu Dec 30 09:55:34 1993 To: hyperchem@autodesk.com Subject: chemplus From: ujordis@email.tuwien.ac.at (Univ. Doz. Dr. Ulrich Jordis, Associate Professor) Reply-To: ujordis@email.tuwien.ac.at Date: Thu, 30 Dec 1993 14:32:42 +0000 Could you please give me information about the ChemPlus module? Sincerely U. Jordis -- ----------------------------------------------------------- Univ.Doz. Dr. Ulrich JORDIS ujordis@email.tuwien.ac.at Assistant Professor Inst. Organic Chemistry, A-1060 Vienna, Getreidemarkt 9, AUSTRIA Tel: +43 1 58801-5013 Fax: +43 1 586 6931