From sjardino@iq.usp.br Wed May 27 08:02:24 1998 Received: from quim.iq.usp.br (quim.iq.usp.br [143.107.46.101]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id IAA23507 Wed, 27 May 1998 08:02:23 -0400 (EDT) Received: (sjardino@localhost) by quim.iq.usp.br (8.6.10/SPARC10-IQ2.0) id IAA23370; Wed, 27 May 1998 08:18:51 -0300 Date: Wed, 27 May 1998 08:17:21 -0300 (EST) From: Sergio Augusto Jardino Filho To: chemistry@www.ccl.net Subject: control panel to XWindows Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Deaar CCL, I have a problem with the use of XWindows in my Macintosh, and what I have detected is the absence of the control panel "sharing setup". Does anyone know where can I download it? Or does anyone who already have it could send it to me? I would become very grateful. Thanks by the atention Sergio A. Jardino Filho Instituto de Quimica - Universidade de Sao Paulo Brazil sjardino@quim.iq.usp.br From gostowskir@apsu01.apsu.edu Wed May 27 16:25:14 1998 Received: from apsu02.apsu.edu (apsu02.apsu.edu [198.146.56.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA26837 Wed, 27 May 1998 16:25:14 -0400 (EDT) Received: from gostowskir.apsu.edu by APSU02.APSU.EDU (PMDF V5.1-4 #16785) with ESMTP id <01IXJ6Y9AFK0006OXX@APSU02.APSU.EDU> for chemistry@www.ccl.net; Wed, 27 May 1998 15:23:26 CST Date: Wed, 27 May 1998 15:27:09 -0500 From: Rudy Gostowski Subject: Gamess error IO-21 To: CCL LIST Message-id: <01IXJ6Y9B0G2006OXX@APSU02.APSU.EDU> MIME-version: 1.0 X-Mailer: Microsoft Internet Mail 4.70.1161 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal I have been getting the error "*ERR* IO-21 invalid STATUS specifier for given file this results when using the input file: The following input file was used: $CONTRL EXETYPE=CHECK MULT=2 COORD=CART UNITS=ANGS $END $DATA 9phflr3.gam 9-PHENYL FLUORENYL RADICAL Cs Carbon 6.0 0.00000 0.00000 0.00000 Carbon 6.0 1.45210 0.00000 0.00000 Carbon 6.0 1.87100 1.38620 0.00000 Carbon 6.0 3.13330 1.97110 0.02490 Carbon 6.0 0.71080 2.24100 0.00220 Carbon 6.0 0.82590 3.61510 0.01050 Carbon 6.0 -0.46680 1.37030 0.00170 Carbon 6.0 2.11040 4.17520 0.02430 Carbon 6.0 3.24470 3.36590 0.03220 Carbon 6.0 2.30380 -1.15170 0.00030 Carbon 6.0 3.49260 -1.17260 -0.75100 Carbon 6.0 1.97210 -2.29760 0.74920 Carbon 6.0 4.31810 -2.29100 -0.75250 Carbon 6.0 -1.82050 1.65300 -0.01070 Carbon 6.0 -0.92770 -1.03650 -0.03470 Carbon 6.0 3.97770 -3.41700 -0.00250 Carbon 6.0 2.80200 -3.41490 0.74910 Carbon 6.0 -2.29160 -0.72800 -0.04420 Carbon 6.0 -2.73650 0.59180 -0.02940 Hydrogen 1.0 -0.59740 -2.08560 -0.06350 Hydrogen 1.0 -3.02640 -1.54770 -0.06870 Hydrogen 1.0 -3.81540 0.80820 -0.03870 Hydrogen 1.0 -2.18180 2.69190 -0.01170 Hydrogen 1.0 4.03960 1.34780 0.05230 Hydrogen 1.0 -0.06500 4.25970 0.01160 Hydrogen 1.0 2.22090 5.27040 0.03150 Hydrogen 1.0 4.24660 3.82060 0.04960 Hydrogen 1.0 5.24200 -2.28820 -1.35090 Hydrogen 1.0 4.63170 -4.30150 -0.00220 Hydrogen 1.0 2.52740 -4.29690 1.34670 Hydrogen 1.0 1.05390 -2.29830 1.35740 Hydrogen 1.0 3.76070 -0.29490 -1.36090 $END Rudy Gostowski Department of Chemistry Austin Peay State University Box 4547 Clarksville, TN 37044 931-648-7624 FAX 931-648-5996 gostowskir@apsu01.apsu.edu From winkler@bellatrix.pcl.ox.ac.uk Wed May 27 04:37:02 1998 Received: from oxmail4.ox.ac.uk (oxmail4.ox.ac.uk [163.1.2.33]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id EAA22676 Wed, 27 May 1998 04:37:01 -0400 (EDT) Received: from bellatrix.pcl.ox.ac.uk by oxmail4 with SMTP (PP); Wed, 27 May 1998 09:36:56 +0100 Received: from bellatrix.pcl by bellatrix.pcl.ox.ac.uk via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id JAA09093; Wed, 27 May 1998 09:36:48 +0100 Date: Wed, 27 May 1998 09:36:48 +0100 (BST) From: Dave Winkler X-Sender: winkler@bellatrix.pcl To: chemistry@www.ccl.net Subject: Re: CCL:Graphs In-Reply-To: <356B604C.C5032F80@patra.netor.gr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII There is the so-called BCUT (Burden, CAS, University of Texas) index invented by Prof. Frank Burden at Monash University and championed by Bob Pearlman and CAS. This takes into account the nature of bonding between atoms. See F.R. Burden, Quant. Struct.-Act. Relat. 16, 309-14 (1997) and F.R. Burden, J. Chem. Inf. Comput. Sci. 29, 225-7 (1994). Cheers, Dave (Dr.) Dave Winkler Visiting Fellow Oxford Centre for Molecular Sciences Oxford University On Wed, 27 May 1998, Koklas Gerasimos wrote: > Hi! > Is there any topological index (like Randic,Balaban,...) that can > include information about double bonds in the system? > > -- > jonarg@patra.netor.gr > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: jonarg@patra.hellasnet.gr > -- Original Sender From: Address: jonarg@patra.hellasnet.gr > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From anina01@iona.cryst.bbk.ac.uk Wed May 27 07:53:04 1998 Received: from pandora.cryst.bbk.ac.uk (pandora.cryst.bbk.ac.uk [192.84.212.49]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA23459 Wed, 27 May 1998 07:53:02 -0400 (EDT) Received: from localhost (anina01@localhost) by pandora.cryst.bbk.ac.uk (8.8.7/8.8.7) with SMTP id MAA10567; Wed, 27 May 1998 12:57:05 +0100 X-Authentication-Warning: pandora.cryst.bbk.ac.uk: anina01 owned process doing -bs Date: Wed, 27 May 1998 12:57:04 +0100 (BST) From: Henrick Alex Ninaber X-Sender: anina01@pandora.cryst.bbk.ac.uk Reply-To: Henrick Alex Ninaber To: chemistry@www.ccl.net Subject: Summary: Correlating data with two or more (Gaussian) distributions Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, This is the summary of responses to my question: ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: The distribution of certain variables I calculate sometimes show more than one mean: in my case this means that the distribution is a sum of two or more separate distributions. Calculating the correlation with (for instance) a single Gaussian distribution does not make much sense. Is anyone familiar with this branch of statistics? I am looking for a theory dealing with this problem. :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: Four responses in total: First response from Peter Shenkin > > How can a single distribution have more than one mean? There > are distributions which do not have a mean, but any distribution > that has a mean has only one. > > Recall that in statistics, the "mean" is a synonym for the "average". > > Are you really trying to say something else? > > -P. Maybe I was trying to say something else. After mailing him personally his second response was: > If you have a reason to expect the underlying distributions to > be Gaussian, or if you just want to use Gaussians to fit your > data, you still have to decide how many to use. Even for data > exhibiting a single mode, if there is some experimental error, > the more Gaussians you use, the better will be your fit. (Just > like fitting points to a polynomial: the more terms you use, > the better will be your fit.) But of course, "better" does > not mean "significantly better", in the statistical sense. > > To fit to N gaussians, you need 3N-1 parameters. Each Gaussian > has a mean and a standard deviation, giving 2N parameters; then > each has an amplitude (fraction it contributes), which would give > another N, except they have to sum to 1; so you have an additional > N-1 instead of N. > > Suppose you try to fit to two Gaussians, using 5 parameters. > I'd start with an initial guess for the parameters from > visualizing the data, then do a minimization in the parameter > space of the RMS deviation of the data points to the sum of the two > Gaussians, starting with your guess. > > If you want to then try with three Gaussians, you can do a > Fisher F test to determine whether the fit is significantly > better as a result of adding the third Gaussian. You can > continue this process until Fisher says that getting fancier > no longer makes the fit significantly better. > > -P. ::::::::::::::::::::::::::::::::::::::::::::::::::::::::: Second response was from David van der Spoel > Hi Alex, > > If you are in fact looking at dihedral angles you may want to have a > look > at my paper: > @Article{Spoel97a, > author = {D. van der Spoel and H. J. C. Berendsen}, > title = {Molecular Dynamics Simulations of {Leu}-Enkephalin in > water and {DMSO}}, > year = 1997, > journal = "Biophysical Journal", > volume = 72, > pages = {2032-2041} > } > > It defines correlation functions for dihedral angles, and does a > comparison to > other forms of such correlation functions in the literature. > > Groeten, David. > ________________________________________________________________________ > Dr. David van der Spoel Biomedical center, Dept. of Biochemistry > s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden > e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel The dihedral angle is one of the properties I need to look at, dank je David, I will get your paper. :::::::::::::::::::::::::::::::::::::::::::::::::: Third response was from Rick Venable > The trick here is to be able to separate the populations, either by > gaussian deconvolution, if the peaks for each mean are well resolved, or > by using additional properties of each data point to resolve the groups > in more than one dimension. Once separated into 2 or more groups, each > group can be analyzed independently. You should also think about > whether having multiple means makes sense for the property you're > calculating, or if perhaps you've just undersampled the underlying > distribution. > > Deconvolution is essentially what goes on in chromatographic data > systems-- peaks are separated into independent populations before > calculating width at half height, integrated area, etc. There's a fair > amount of older literature on deconvolution of Gaussian, Lorentzian, and > other distributions, and probably some good book chapters; I don't have > refs handy (I'm at home), but could provide some on request. > > Deconvolution is essentially what goes on in chromatographic data > systems-- peaks are separated into independent populations before > calculating width at half height, integrated area, etc. There's a fair > amount of older literature on deconvolution of Gaussian, Lorentzian, and > other distributions, and probably some good book chapters; I don't have > refs handy (I'm at home), but could provide some on request. > > Using additional properties to resolve the groups in a higher > dimensional space is another possibility; discriminant analysis is often > used to treat this problem by statisticians. For each data point in > your distribution, you need several additional properties. A least > squares fit in N-dimensional space tells which of the N properties offer > the most discrimination; 2D scatter plots of the more significant > properties may show clear groupings. Commercial stat packages have > modules for this, and I wouldn't be surprised to discover freely > available Fortran or C code. Gaussian deconvolution is the theory I was looking for, I will get articles on it myself. :::::::::::::::::::::::::::::::::::::::::::::: Last person to answer the question was Jack Smith: > You might look into the way polymer scientist characterize molecular > weight distributions (MWD) using polydispersity indices (PDI), which > often display bimodality (two peaks). The polydispersity index is a > ratio of two types of averages (weight average and number average). The > MWD can be described by even higher "moments". When MWD's are truly > composite (and now just broad), there are various ways to deconvolute > composite MWD's into separate "normal" MWD's using such moment > expansions. > > - Jack The package Origin is able to do some 'multipeak splitting' but is not flexible enough: I have to give initial values for the Gaussians, which doesn't speed up the process. I want to code it myself anyway (using someone's theory how to do it properly). Thank you all very much for responding, I think I have a fairly good idea now how to solve the problem. Alex Ninaber From evaldera@maria.ivic.ve Wed May 27 13:26:00 1998 Received: from maria.ivic.ve (root@maria.ivic.ve [150.186.8.27]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA25787 Wed, 27 May 1998 13:25:59 -0400 (EDT) Received: from localhost (evaldera@localhost) by maria.ivic.ve (8.8.7/8.8.7) with SMTP id NAA09887; Wed, 27 May 1998 13:21:16 GMT Date: Wed, 27 May 1998 13:21:16 +0000 (GMT) From: Elmer Valderrama To: ccl Subject: Re: summary: molecular builder In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Another possibility is to use Wine (Windows 3.1 emulator) to run HyperChem 3.0 (TM) for W3.1 under your Unix box (e.g. linux,irix,aix) I've tested this way with a dual PPro under linux with good results. (babel must be installed for converting to other formats). Elmer On Mon, 25 May 1998, Rochus Schmid wrote: > > > > > hi netters, > > thanks to all who responded to my question. > > there is not much to summarize and I won't list all the answers I've got > here. Most replies are roughly: > "we've been looking for that kind of software, too. Couldn't find > anything." > > > BUT: > I was pointed to molden3.3 > http://www.caos.kun.nl/~schaft/molden/molden.html > > and looked at it again. > > It's not exactly what I wanted but it's worth to consider. The problem is: > you can easily edit a z-matrix with it. but in order to change *any* > internal coordinate this must be defined in terms of the z-mat. so if I > start from xyz and the auto z-mat builder doesn't make a z-mat which > includes this int. coordinate I have to reedit the whole z-mat. > > this is all I have, sorry ;-) > > greetings, > > rochus > > > P.S. > what about if all those people (including me), who want to have such a > software think about "creating" it? > I was thinking about using a openGL extended scripting language like > tcl (or maybe python) for the job. since I have no clue about tcl I was > wondering if someone could supply a "viewport" which just displays a ball > and stick model which can be rotated etc.? > if you want to comment this idea or have any (definetly better ;-) ones > please reply *directly* to me, since we don't want to waste the bandwidth > on ccl. > > > > On Tue, 12 May 1998, Rochus Schmid wrote: > > > > > > > > > > > Dear Netters, > > > > Please forgive me for asking that question, which came up a couple of > > times already, I know. But I am desperate and my question is rather > > specific: > > > > I am searching for a (simple!!!, 3D!) molecular builder: > > > > - it should run under UNIX/X and be free (I know cerius2 and insightII > > and and and ....) > > > > - it should be very simple (I don't need ruberbands, rayshading etc. and > > it is only for a couple of atoms and not for > > proteins) > > > > - it should be able to add or delete atoms by mouse and change bond > > length, angles and dihedrals by selecting the atoms. > > > > - it should be able to read and write the stuff as pdb or xyz or whatever > > > > > > > > I follow this mailing list for quite a while now and similar questions > > came up quite often, I know. > > > > So I know about gopenmol and xmol and viewmol and molden and vmd and a > > couple more. But none of these programs is what I'm looking for. > > > > To make that more clear: > > I really like xmol. It's simple and free etc. but you can't build > > molecules. > > > > And I really liked the UNICHEM interface by Cray. This was perfect to me > > but it is not free ;-) > > > > Is there anything on this beautifull world like that?? > > I can't believe, that I'm the only one who needs that kind of software. > > > > Thanks in advance for any comment or hint. > > Happy computing, > > > > > > Rochus > > > > > > > > > > ******************************************************************** > > Rochus Schmid Phone: (403) 220-3232 > > University of Calgary Fax: (403) 289-9488 > > Department of Chemistry Email: rschmid@acs.ucalgary.ca > > 2500 University Drive N.W. > > Calgary, Alberta > > Canada T2N 1N4 > > http://www.chem.ucalgary.ca/groups/ziegler/ > > ******************************************************************** > > > > > > > > --- > > Administrivia: This message is automatically appended by the mail exploder: > > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > > Web: http://www.ccl.net/chemistry.html > > --- > > > > > > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > From yubofan@guomai.sh.cn Wed May 27 22:51:43 1998 Received: from guomai.sh.cn ([202.96.206.69]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id WAA28683 Wed, 27 May 1998 22:51:38 -0400 (EDT) Received: from guomai.sh.cn (Email-10 [210.0.0.10]) by guomai.sh.cn (8.8.8/8.8.8) with ESMTP id KAA02450 for ; Thu, 28 May 1998 10:49:38 +0900 (CDT) Message-ID: <356CD065.E0DEA075@guomai.sh.cn> Date: Thu, 28 May 1998 10:48:05 +0800 From: Yubo Fan Reply-To: yubofan@guomai.sh.cn Organization: Department of Chemistry, Fudan University X-Mailer: Mozilla 4.04 [en] (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Cyclodextrin. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, everyone, I have been looking for the structure of cyclodextrin in the Web but failed. Is there cyclodextrin structure file (for example, PDB file) in the InterNet? Or, if someone have, could you please send me one copy by email? I need the structures of alpha-cyclodextrin, beta-cyclodextrin and gamma-cyclodextrin. The precise structure data is preferred, for instance, the data from monocrystal or by calculation. With best regards Y. Fan -- ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab yubofan@fudan.edu.cn The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China =============================================================