From ns14@crux3.cit.cornell.edu Wed May 19 22:01:35 1993 Date: Thu, 20 May 93 02:01:35 -0400 From: ns14@crux2.cit.cornell.edu Message-Id: <9305200601.AA26657@crux3.cit.cornell.edu> To: chemistry@ccl.net Subject: Re: 3D to 2D ball and stick models >>> On Wed, 19 May 1993 17:01:03 -0500, jas@medinah.atc.ucarb.com (Jack Smith) said: >I have alot of MacroModel molecule files which I would like to >display in memos and journal articles. For those places that color >CPK displays are appropriate, a screen image is fine. However, >for black and white photocopies and many memos, a 'ORTEP-like", or >"ball and stick" representation with hidden line removal would be best. > >Does anybody have suggestions for how to do this with PC software, >or Unix software, preferably resulting in postscript output? > JS> I find MSC XMol's output quite sufficient. CAChe's "Schematic" print JS> option is also quite good. There are also various ORTEP programs (like JS> NAMOD from QCPE) floating around. I'm fighting with this right now, for my phud thesis. So far I prefer the program Molscript. It runs on unix boxes, preferably sgi. Xmol doesn't seem to let you put labels in, which I need; otherwise it may have been my choice. The bad parts about molscript: If you don't have a postscript previewer on hand you will go crazy; no interactive display, and you'll have to rotate the molecule in a script file. Also, you would *think* that these programs could fairly easily place labels so they don't overlap.... (molscript let's you place them by hand, in the script file, to partially overcome this problem) Oh yes: If you like macs and have it/can buy it, Chem3d is probably your best bet. It writes EPS files, and I believe the newer versions read macromodel files. I hate macs but acknowledge their good points :) just my 0.02 nathan From raman@bioc01.uthscsa.edu Thu May 20 03:30:19 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9305201330.AA01597@bioc01.uthscsa.edu> Subject: 3D- To: models@ccl.net, chemistry@ccl.net Date: Thu, 20 May 1993 08:30:19 -0500 (CDT) > The bad parts about molscript: If you don't have a postscript > previewer on hand you will go crazy; no interactive display, and > Well, I have already reviewed MOLSCRIPT in one of my previous postings and has been ported to work on different platforms. With respect to the availability of postscript previewer, there are two very nice programs that do the same (in the Public Domain): GHOSTSCRIPT and GHOSTVIEW. Use Archie to find the site that distributes it. -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** All Science is either Physics or stamp collecting -E.Rutherford ****************************************************************************** From raman@bioc01.uthscsa.edu Thu May 20 03:31:39 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9305201331.AA01617@bioc01.uthscsa.edu> Subject: 3D To: to@ccl.net, 2D@ccl.net, chemistry@ccl.net Date: Thu, 20 May 1993 08:31:39 -0500 (CDT) > The bad parts about molscript: If you don't have a postscript > previewer on hand you will go crazy; no interactive display, and > Well, I have already reviewed MOLSCRIPT in one of my previous postings and has been ported to work on different platforms. With respect to the availability of postscript previewer, there are two very nice programs that do the same (in the Public Domain): GHOSTSCRIPT and GHOSTVIEW. Use Archie to find the site that distributes it. -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** All Science is either Physics or stamp collecting -E.Rutherford ****************************************************************************** From chiremv!andromeda!jeffb@uunet.UU.NET Thu May 20 07:59:07 1993 Date: Wed, 19 May 93 23:33:25 -0700 From: chiremv!andromeda!jeffb@uunet.UU.NET (Jeff Blaney) Message-Id: <9305200633.AA06574@andromeda> To: uunet!ccl.net!chemistry-request@uunet.UU.NET Subject: Re: Structure display from SMILES Daylight Chemical Information Systems has some X-windows utilities that display 2D-depictions (and create postscript output) from SMILES input on UNIX workstations. Mac-X running on a Mac-IIci or better provides good X-windows performance. I'm not aware of any currently available Mac stand-alone programs that perform 2D or 3D-depictions from SMILES. Jeff Blaney Chiron From doherty@msc.edu Thu May 20 04:54:13 1993 Message-Id: <9305201554.AA26835@uh.msc.edu> Date: Thu, 20 May 1993 10:54:13 -0600 To: ns14@crux2.cit.cornell.edu, chemistry@ccl.net From: doherty@msc.edu (David C. Doherty) Subject: Re: 3D to 2D ball and stick models very early one morning, nathan (ns14@crux2.cit.cornell.edu) wrote: NS>Jack Smith (jas@medinah.atc.ucarb.com) wrote: JS>Tom Pierce (rs0thp@RohmHaas.Com) wrote: TP>I have alot of MacroModel molecule files which I would like to TP>display in memos and journal articles. For those places that color TP>CPK displays are appropriate, a screen image is fine. However, TP>for black and white photocopies and many memos, a 'ORTEP-like", or TP>"ball and stick" representation with hidden line removal would be best. TP> TP>Does anybody have suggestions for how to do this with PC software, TP>or Unix software, preferably resulting in postscript output? TP>... > JS> I find MSC XMol's output quite sufficient. CAChe's "Schematic" print JS> option is also quite good. There are also various ORTEP programs (like JS> ... NS> I'm fighting with this right now, for my phud thesis. So far NS>I prefer the program Molscript. It runs on unix boxes, preferably NS>sgi. Xmol doesn't seem to let you put labels in, which I need; NS>otherwise it may have been my choice. NS>... NS>(some stuff about molscript...) NS>... NS> I hate macs but acknowledge their good points :) I'll add a few suggestions that I hope will be generally useful (and not just relevant to XMol). Unfortunately for Nathan, two of them involve the Mac. I assume that when he says "labels," Nathan is referring to "annotation" generally. In the spirit of the "tools" versus "kitchen sinks" discussions of late, the intent of our XMol design was decidedly more in line with the former rather than the latter. The fact that the EPS output from XMol can be considered "quite sufficient" is good; yet we acknowledge that as a tool for preparing figures, XMol is not as flexible as some might desire. Now that I've identified the problem, let me suggest some other "tools" that, used in conjunction with the XMol tool (and others...), might provide a solution. Note that there may be variants of these procedures that work as well on the PC or Unix boxes as on the Mac (I happen to like Macs but acknowledge their weaknesses :). 1. Recognize that Postscript is a programming language. Recognize also that Postscript files are ascii. Whip out your favorite text editor and have a go........OK, OK, this is clearly a last resort. However, if you just want a few labels here and there, and you have just a *little* knowledge of what you're doing, this can be effective. 2. This one will sound like a lot of work. That is because it makes use of many "tools." Fortunately, once they are in place, the use of these tools can be simplified by sheparding them via some simple scripts and Unix pipes, and the quality of the resulting figures is worth the effort of setting everything up. Note that this solution makes use of many freely available tools. One of the features of EPS (encapsulated postscript) files is that they can (optionally) include an embedded "raster" preview. In other words, in addition to all of the postscript drawing commands, there is a section defining a bitmap image of the postscript page. Most Macintosh drawing programs (PC too, I assume) don't directly interpret the Postscript commands and render them with QuickDraw calls. Some can, however, read in these commands and pass them on to a postscript printer later. Generally, when you read in a postscript file without a preview, all you see is a "greeked" version of the page - a big X enclosed by a box or the like. If the EPS file contains a bitmap preview (PICT, in the case of the Macintosh), these programs will display it, rather than the big X. You can then proceed to annotate to your heart's delight, and when you print, you will get the original postscript image (the bitmap preview is ignored when printing), with your annotations overlaid. So you get the benefit of the resolution of the original postscript, along with the ability to annotate. (My program of choice for this purpose is MacDraw Pro v1.5 from Claris). So how does one go about embedding a PICT preview in an EPS file? A fellow at UPenn named George Jefferson has created a nice package for doing just this on your Unix box. It is freely available at: sumex-aim.stanford.edu as info-mac/unix/ps2eps-13.shar He includes a description of how to install and run it. It requires a few of the pbmplus raster conversion tools(!), which can be found by asking archie. Ghostscript is required also. Note: Mr. Jefferson does not recommended that you try to read his source code (it just works). After you transfer the file to your mac, you will need to change its type to 'PICT' in order for programs like MacDraw Pro to be able to read it. There are many tools available at sumex to do this also. 3. The Ghostscript package is now also available on the Macintosh (at sumex also). A nice feature is that it can convert the Postscript page to a series of QuickDraw commands (PICT), and save the result to a file. Unfortunately, Ghostscript renders circles as a series of (albeit short) line segments. Those looking for high resolution (which is where this whole discussion started) will recognize that this is a serious drawback in our field. This discussion has turned out to be much longer than I intended, but hopefully it will help those of you out there who have ruefully said to yourselves, "I sure wish that I could annotate that Postscript file." Now a quick question: Does anyone out there know the origin of the term "Image Greeking?" Happy figure making... Dave Doherty p.s. For those who don't know: XMol v1.3.1 is available at: ftp.msc.edu, in the pub/xmol directory. Download the "README" file for directions. --- David C. Doherty Minnesota Supercomputer Center, Inc. doherty@msc.edu From B314U05@UTARLG.UTA.EDU Mon May 20 11:34:54 1993 Date: 20 May 1993 16:34:54 -0500 (CDT) From: B314U05@UTARLG.UTA.EDU Subject: cart-Zmat To: chemistry@ccl.net Message-Id: <01GYEL65IJKI0003UL@UTARLG.UTA.EDU> Hello Everybody Could somebody please send me the program which converts cartesian coordinates to Z-mat form. If not, could you please tell me where to get the program. Thanks in advance pavankumar e.mail: b314u05@utarlg.uta.edu