From rochus@felix.anorg.chemie.tu-muenchen.de Wed May 8 08:51:36 1996 Received: from felix.anorg.chemie.tu-muenchen.de for rochus@felix.anorg.chemie.tu-muenchen.de by www.ccl.net (8.7.1/950822.1) id IAA09161; Wed, 8 May 1996 08:18:00 -0400 (EDT) Received: by felix.anorg.chemie.tu-muenchen.de (940816.SGI.8.6.9/930416.SGI) for chemistry@www.ccl.net id OAA26046; Wed, 8 May 1996 14:17:49 +0200 From: "Rochus Schmid" Message-Id: <9605081417.ZM26044@felix> Date: Wed, 8 May 1996 14:17:48 -0600 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: processing of HPGL-files Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Netters, I have a question which is (in my eyes) related to CC: How to get nice pictures of calculated molecules? I usually use SCHAKAL to produce HPGL-plots. After that I label these plots and plug in some bond distances or so. This can be done nicely on the PC with Word for Windows. My problem is: I would like to do that on the workstation. My question is: Is there any free software (UNIX) to manipulate HPGL-files or some fileformat HPGL can be converted into (e.g. SGI-showcase) to process it? Or is there any alternative to SCHAKAL? How do you prepare the artwork for publications? I would be happy about every suggestion. Thank you in advance. Best greatings, Rochus -- ******************************************************************************** Rochus Schmid Technische Universitaet Muenchen Tel. ++49 89 3209 3140 Anorganisch Chemisches Institut 1 Fax. ++49 89 3209 3473 Prof. W. A. Herrmann E-mail: Lichtenbergstrasse 4 rochus@felix.anorg.chemie.tu-muenchen.de 85747 Garching ******************************************************************************** From VKPIDUGU+aCENTRAL%Armstrong@mcimail.com Wed May 8 09:51:36 1996 Received: from gatekeeper.mcimail.com for VKPIDUGU+aCENTRAL%Armstrong@mcimail.com by www.ccl.net (8.7.1/950822.1) id JAA09566; Wed, 8 May 1996 09:33:39 -0400 (EDT) Received: from mailgate.mcimail.com (mailgate.mcimail.com [166.38.40.3]) by gatekeeper.mcimail.com (8.6.12/8.6.10) with SMTP id NAA11720; Wed, 8 May 1996 13:28:57 GMT Received: from mcimail.com by mailgate.mcimail.com id cb28960; 8 May 96 13:31 WET Date: Wed, 8 May 96 08:29 EST From: "Pidugu, Vijaya K" To: chemistry net Subject: Modeling cellulose Message-Id: <34960508132943/0003048861DC1EM@MCIMAIL.COM> From: Vijaya K Pidugu at notes1 1996/05/08 09:24 Subject: Modeling cellulose To: MCI at central -------------------------------- Message Contents ------------------------------ To: MCI cc: From: Vijaya K Pidugu @ ARMSTRONG Date: 05-08-96 09:24:02 AM Subject: Modeling cellulose Can anyone who has modeled cellulose share their experience with me? If there is a way to obtain the coordinates for cellulose crystal (from x-ray diffraction studies) that will perhaps solve my problem. Thank you. Vijaya Kumar Pidugu Armstrong World Industries, Inc. P.O. Box 3511, 2500 Columbia Avenue Lancaster, PA 17604 email vkpidugu+aCENTRAL%ARMSTRONG@MCIMAIL.COM email vijaya@xeno.chem.psu.edu From owner-chemistry@ccl.net Wed May 8 10:51:38 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id KAA10076; Wed, 8 May 1996 10:51:14 -0400 (EDT) Received: from camsci.com for jsb2@camsci.com by bedrock.ccl.net (8.7.1/950822.1) id KAA26111; Wed, 8 May 1996 10:51:11 -0400 (EDT) From: Date: Wed, 8 May 96 10:28:52 EDT Received: by camsoft.com (4.1/3.1.090690-Cambridge Scientific Computing) id AA25689; Wed, 8 May 96 10:28:52 EDT Message-Id: <9605081428.AA25689@camsoft.com> To: R29CLOSE@ETSU.EAST-TENN-ST.EDU, chemistry@ccl.net Subject: Re: CCL:Adding H-atoms?? [following up to my own message...] >> For example, one can convert crystallographic xyz coordinates into >>ALCHEMY input with BABEL. But this conversion involves looking at >>the "bonding nature" of the atoms and doesn't seem to work if the >>hydrogen atoms are missing. > >This is a deficiency of Babel, not Alchemy. I have had two people attack me for making this statement, and it's still early morning. Sigh. Let me try again: "If true, this is a deficiency of Babel, not Alchemy" Does that make everyone happy? The original poster seemed like a fairly intelligent fellow who made a good effort to solve his own problem before posting to this list. From his post, I thought it reasonable to assume that he had attempted several of the more-obvious solutions, including changing the conversion parameters within Babel. I have not had extensive experience with Babel, so I took his word for it. I find it somewhat disappointing that neither of the people who saw fit to criticize me have decided themselves to post any information that would actually help the original poster. (At least, nothing has reached me yet. The way things are going, their posts and this post will cross in the ether.) So chill out, folks! Jonathan Brecher CambridgeSoft Corporation jsb@camsoft.com From herrmann@hermes.informatik.uni-stuttgart.de Wed May 8 11:51:49 1996 Received: from ifi.informatik.uni-stuttgart.de for herrmann@hermes.informatik.uni-stuttgart.de by www.ccl.net (8.7.1/950822.1) id LAA10253; Wed, 8 May 1996 11:14:59 -0400 (EDT) Date: Wed, 8 May 1996 17:14:22 +0200 Message-Id: <199605081514.RAA11393@odysseus.informatik.uni-stuttgart.de> Received: by odysseus.informatik.uni-stuttgart.de; Wed, 8 May 1996 17:14:22 +0200 From: Frank Herrmann To: rochus@felix.anorg.chemie.tu-muenchen.de CC: chemistry@www.ccl.net In-reply-to: <9605081417.ZM26044@felix> (rochus@felix.anorg.chemie.tu-muenchen.de) Subject: Re: CCL:processing of HPGL-files Dear Rochus, I use the following (free) viewers with and without the abbility to output postscript (see below). For those without one can use xv to grab part of the screen and convert to postscript. Sometimes it's necessary to add bounding boxes (using bbfig) to include the figures in documents (e.g. using psfig in latex). postscript output: xmol (good for small molecules) rasmol (good for bigger molecules) moil-view (sgi) no postscript output: flex vmd (sgi, raytracer output) Hope this helps, ----------------------------------------------- Frank Herrmann, Computer Scientist, PhD Student Dept. of Molecular Biophysics 0810 German Cancer Research Center Im Neuenheimer Feld 280, D-69120 Heidelberg Tel: (49) 6221-422336, FAX: (49) 6221-422333 email: Herrmann@odysseus.informatik.uni-stuttgart.de From owner-chemistry@ccl.net Wed May 8 12:51:44 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id LAA12086; Wed, 8 May 1996 11:51:42 -0400 (EDT) Received: from gatekeeper.tripos.com for dlarson@thebe.tripos.com by bedrock.ccl.net (8.7.1/950822.1) id LAA27084; Wed, 8 May 1996 11:51:35 -0400 (EDT) Received: (from news@localhost) by gatekeeper.tripos.com (8.6.12/8.6.12) id KAA15163; Wed, 8 May 1996 10:51:33 -0500 Received: from tripos.tripos.com(192.160.145.1) by gatekeeper.tripos.com via smap (V1.3) id sma015161; Wed May 8 10:51:17 1996 Received: from thebe.tripos (thebe.tripos.com [192.160.145.47]) by tripos.tripos.com (8.6.12/8.6.12) with SMTP id KAA10176; Wed, 8 May 1996 10:50:43 -0500 Received: by thebe.tripos (920330.SGI/5.6) id AA14840; Wed, 8 May 96 10:50:42 -0500 Date: Wed, 8 May 1996 10:50:42 -0500 (CDT) From: David Larson Sender: David Larson Reply-To: David Larson Subject: Re: CCL:Adding H-atoms?? To: R29CLOSE@ETSU.EAST-TENN-ST.EDU Cc: chemistry@ccl.net In-Reply-To: <01I4F5T5Y9EA8X1NSB@phem3.acs.ohio-state.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Alchemy will import crystal coordinate data using the File >> Crystal... command. The file format can be found on p91 of the the Alchemy manual. Another alternative is to convert it to pdb format and then import it into Alchemy. If you have any questions or problems please let me know. Cheers, Dave ---------------------------------------------------------------------------- David Larson Email: dlarson@tripos.com Customer Support Scientist Phone: 314 647 1099 TRIPOS Inc FAX: 314 647 9241 St Louis MO 63144 ---------------------------------------------------------------------------- From owner-chemistry@ccl.net Wed May 8 22:51:42 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id VAA16631; Wed, 8 May 1996 21:55:13 -0400 (EDT) Received: from mailbox.syr.edu for wtwinter@MailBox.Syr.Edu by bedrock.ccl.net (8.7.1/950822.1) id VAA04670; Wed, 8 May 1996 21:55:12 -0400 (EDT) Received: from hydra.syr.edu (wtwinter@hydra.syr.edu [128.230.1.33]) by mailbox.syr.edu (8.7.5/8.7.3) with ESMTP id VAA18542; Wed, 8 May 1996 21:55:10 -0400 (EDT) Received: (from wtwinter@localhost) by hydra.syr.edu (8.7.5/8.7.3) id VAA07534; Wed, 8 May 1996 21:54:35 -0400 (EDT) Date: Wed, 8 May 1996 21:54:33 -0400 (EDT) From: "William T. Winter" To: jsb2@camsoft.com cc: R29CLOSE@ETSU.EAST-TENN-ST.EDU, chemistry@ccl.net Subject: Re: CCL:Adding H-atoms?? In-Reply-To: <9605080136.AA22903@camsoft.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 7 May 1996 jsb2@camsoft.com wrote: > > > I need to know how to add hydrogen atoms to a large crystallographic > >structure that does not report the hydrogen atom positions. > > Programs like ALCHEMY have an "add H" option that is useful in > >drawing structures, but I can't find a good way to get the coordinates > >into ALCHEMY. This request seems a little odd since Alchemy has a "crystal input" option Using it is fairly simple, you need the unit cell parameters, found in the abstract and again in a small table, in any standard crystal structure report. then you need the coordinates, and you have to change the namesd of the atoms from those given in the paper to atom types recognized by alchemy. These are listed in the manual or if you do not have it they can be found in the file "atomdef.tab" in the "tables" directory. Alchemy even includes a a sample of a crystal input file, it has the file extension ".cry". Finally, you can also use the crystal input routine to input cartesian coordinates by setting the a=b=c=1.00 and alpha=beta=gamma=90.0 on the lattice constant card. Once the structure is in you can then add hydrogens in alchemy. This is also a convenient route into other modeling programs since alchemy can write mm2 and sybyl file structures. If you need other sample files I can provide them but not for peptides. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Dr. William T. Winter Phone: (315)470-6876 315 Baker Lab FAX: (315)470-6856 SUNY-ESF Internet: wtwinter@mailbox.syr.edu Syracuse, NY 13210-2786 URL http://www-chem.esf.edu