From chemistry-request@server.ccl.net Sat Jul 22 04:36:46 2000 Received: from mailcity.com (fes-qout.whowhere.com [209.185.123.96]) by server.ccl.net (8.8.7/8.8.7) with SMTP id EAA19249 for ; Sat, 22 Jul 2000 04:36:46 -0400 Received: from Unknown/Local ([?.?.?.?]) by mailcity.com; Fri Jul 21 06:29:31 2000 To: chemistry@ccl.net Date: Fri, 21 Jul 2000 06:29:31 -0700 From: "Darren Fayne" Message-ID: Mime-Version: 1.0 X-Sent-Mail: on Reply-To: fayned@lycos.com X-Mailer: MailCity Service Subject: Summary: Creating a movie of a moving molecule X-Sender-Ip: 136.206.1.19 Organization: Lycos Communications (http://comm.lycos.com:80) Content-Type: text/plain; charset=us-ascii Content-Language: en Content-Transfer-Encoding: 7bit Hi cclers, I have just noticed Damian Scherlis' question and it occurred to me that I had never posted a summary of an enquiry I had sometime back. Apologies to anyone who was eagerly awaiting it (particularily Anita)!!! My initial question Hi all, I've a quick question for you guys. I am wondering how to create a movie of a molecule that I have rotated and moved for inclusion in a PowerPoint presentation? Preferably freeware that runs under Windows 95, but I also have access to IRIX 6.3. Any personal experience on what you consider to be the best software would be much appreciated. Thanks in advance, Darren Fayne Unfortunately I did not have much time to delve into all the different options available but what worked well for me was screen capturing the image of my molecule as I slowly rotated/moved it. Paintshop Pro converted the rgbs to jpgs. Then the Paint Shop Pro 6 animation shop was used to piece the images together and create an avi. -------------------------------------------------------------------------------------------------- Here is the replies that I received for which I am very grateful. I'm sure they will be of interest to many people as a major hurdle in getting your scientific infomation across is actually catching the audience's attention and showing them the 3D aspects of your molecule/reaction! Short term solution (as you want freeware!), this is what I did (not saying it's the best way ...) Get WebLab (www.msi.com) import individual frames, size / render them and export as jpegs, then render them into a movie with animation software (I used JASC Animation Shop for a quick fix). Nice results, but doesn't really help for long-term solutions as a freeware solution. Other things I've tried are MolMol (www.bio.ethz.ch ??) vmd (www.ks.uiuc.edu) and gOpenMol (www.csc.fi/~laaksonen ??) to get fairly nice renderings, but WebLab gives the nicest result (for my needs, anyway). I also put PoVRay between WebLab and the movie renderer to get *even nicer* results. I have been working in an art college (not doing 'molecular art' or other such cliched things(!)) and it's not really *that* much easier making a movie with the 'proper' software (Premiere, etc) than it is to do 'in your bedroom' as it were. If you need a hand, let me know if I can help! Simon Hogg ------------------------------------------------------------------------------------------------- ON a sgi it's easy. 1.) generate the configs you want to animate and save in a PDB file 2.) use Rasmol (freeware) to image the configs, write a rasmol script to do any rotations, shading, etc...that you want and generate a gif image. this you have to do by hand for one of the files to get the image to look the way you want it to look. I have a shell script which does this as a batch job once I get it set on the first config. The key is to use rasmol to generate gif images. What you wind up with is a set of gif images of the system at various time frames. 3.) then use moviemaker (on the SGI) to string together the gif images and save as a quicktime movie. 4.) power-point away I've also used Mathematica to generate movies....which is easy as well. Eric R Bittner, Asst. Professor ph: 713-743-2775 Dept. of Chemistry fax:713-743-2709 University of Houston, Houston TX 77204 email: bittner@uh.edu http://eiger.chem.uh.edu/bittner/index.html ------------------------------------------------------------------------------------------------- Darren, I've got a collection of movies that I created with a combination of RasMol, Molscript, Raster3D and perl script, http://www.bmm.icnet.uk/people/turcotte/resources/ Marcel Turcotte Biomolecular Modelling Laboratory M.Turcotte@icrf.icnet.uk Imperial Cancer Research Fund Phone/Fax +[44]-(020)-7269-3348/3258 PO Box 123, 44 Lincoln's Inn Fields http://www.bmm.icnet.uk/people/turcotte London WC2A 3PX, England ------------------------------------------------------------------------------------------------- Dear Darren, you can include molecules built with WebLab Viewer in your presentation. You can even start it from your ppt presentation and rotate etc. the molecule while giving the presentation. A light version of the WebLab Viewer is downloadable for free at http://www.msi.com Best regards Klaus Klaus Stark,PhD Application Scientist Molecular Simulations Inc. Inselkammerstr. 1 82 008 Unterhaching-Muenchen Germany Phone : 0049-89-61459-420 Mobile : 0049-172-936-3380 Fax : 0049-89-61459-400 E-Mail : kstark@msi.de Web Page : http://www.msi.com ------------------------------------------------------------------------------------------------- Dear Darren, I have spent some time around this subject. Finally the best way (for me) is the use of both WeblabViewer pro (available on the MSI web site) and Paint shop pro 6. They are not freeware but you can try the demo versions. With Weblab, you can transform automaticaly many coordinate files (in various format) in hight quality pictures by using the integrated script language. I can send you a exemple of a script. The second step is performed with the animation module of paint shop which allows to create a movie provided that AVI is the saving format. Microsoft AVI file seems to be the best for a Powepoint presentation. In my case, a full screen hight quality movie with 130 frames takes 10 Mo and runs fine on my notebook. Hope this help. Eric Vangrevelinghe, PhD. ------------------------------------------------------------------------------------------------- Dear Darren: I am not sure of how this would be done, and so I would be interested if you could post a summary of the answers received -- when such a summary becomes available. Recently, I have had to produce two animations for a Web page using animated gifs and/or Macromedia flash. It works well on the Web page, but I have not tried importing these into Powerpoint. Seeing if Powerpoint could handle these types of files would be something that I would first check out. Best wishes on a speedy solution, Anita Zvaigzne ------------------------------------------------------------------------------------------------- I use GIMP to make animated GIFs. I think there is a version of GIMP for Windows, and I hope that PowerPoint knows about animated GIFs, but I have zero experience with Windows. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- Hi Darren One, laborious, way could be the following: Draw the molecule in successive stages of rotation, saving each time as a *.gif. Then import into Powerpoint and use the animation feature to create the movie. This works OK for Cerius2, hwoever that's not freeware :-( Try IsisDraw maybe (www.mdli.com) or do a search.. Micko Mr. Michael Nolan BSc. MEngSc. Aldo's SuperWhiteArmy NMRC (Ireland's ICT Research Center), Lee Maltings, Prospect Row, Cork, IRELAND mail: michael.nolan@nmrc.ie; http://www.nmrc.ie; http://trfc.editthispage.com Tel: + 353 21 4904113; Fax: +353 21 4270271 ------------------------------------------------------------------------------------------------- Hi Darren, The best thing is to convert it to a .mpeg file and embed that into you powerpoint presentation. As long as the .mpeg file is in the same directory you can run the movie within the presentation. There are quite a few .mpeg players and file converters available. The standard SGI mediatools (movieconvert and mediaplayer are good enough to create .mpeg files). Hope this helps, Shyam ------------------------------------------------------------------------------------------------- Hi Darren, I did some movies with molden http://www.cmbi.kun.nl/~schaft/molden/molden.html and it was working fine at least on unix systems. I know that also gOpenMol is able to create movies but you will need a set of coordinates to create the "movement" (I think). http://www.csc.fi/~laaksone/gopenmol/gopenmol.html ciao Fabio ---|Fabio Mariotti|--------o00o--<-><->--o00o---------------------------------- Department of Inorganic Chemistry http://www-chem.unifr.ch/ac/phd/fmariotti/ Univ Fribourg (Suisse) Perolles mailto:fabio.mariotti@unifr.ch Tel: ++41 26 300 8752 Fax: ++41 26 300 9738 --- Darren Fayne College phone: 00-353-1-7048193 Mobile: 086-8304090 Alternative E-mail: fayned@yahoo.com 95970665@tolka.dcu.ie School of Chemical Sciences, Dublin City University, Dublin, Eire. Get your FREE Email and Voicemail at Lycos Communications - http://comm.lycos.com From chemistry-request@server.ccl.net Sat Jul 22 11:24:40 2000 Received: from postoffice.igalaxy.net (postoffice.igalaxy.net [64.160.104.184]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA21599 for ; Sat, 22 Jul 2000 11:24:40 -0400 Received: from hpotter.vaughan.home [64.160.106.118] by postoffice.igalaxy.net with ESMTP (SMTPD32-6.00) id AE1333900098; Sat, 22 Jul 2000 08:30:27 -0700 Received: from daddy by hpotter.vaughan.home with local (Exim 3.12 #1 (Debian)) id 13G18Z-0000DY-00; Sat, 22 Jul 2000 08:24:23 -0700 Date: Sat, 22 Jul 2000 08:24:23 -0700 From: Kenward Vaughan To: Darren Fayne , chemistry@ccl.net Subject: Re: CCL:Summary: Creating a movie of a moving molecule Message-ID: <20000722082423.A701@igalaxy.net> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii User-Agent: Mutt/1.0.1i In-Reply-To: ; from fayned@lycos.com on Fri, Jul 21, 2000 at 06:29:31AM -0700 Sender: Kenward Vaughan Sorry to also walk in on this a bit late, but a graphics modeling program I particularly like is Spock by Jon Christopher ( http://quorum.tamu.edu/jon/spock ). It works on a number of platforms, including Linux (my flavor :), and has very nice facilities to carry out a variety of tasks, including the creation of movies. Jon has been incredibly helpful over the past years whenever I had questions, and I have been very impressed with the capabilities of his program. Kenward Vaughan Bakersfield College (currently home for the summer :) On Fri, Jul 21, 2000 at 06:29:31AM -0700, Darren Fayne wrote: > Hi cclers, > I have just noticed Damian Scherlis' question and it occurred to me that I had never posted a summary of an enquiry I had sometime back. Apologies to anyone who was eagerly awaiting it (particularily Anita)!!! > > My initial question > > Hi all, > I've a quick question for you guys. I am wondering how to create a movie of a molecule that I have rotated and moved for inclusion in a PowerPoint presentation? > Preferably freeware that runs under Windows 95, but I also have access to IRIX 6.3. > Any personal experience on what you consider to be the best software would be much appreciated. > Thanks in advance, > Darren Fayne > > Unfortunately I did not have much time to delve into all the different options available but what worked well for me was screen capturing the image of my molecule as I slowly rotated/moved it. Paintshop Pro converted the rgbs to jpgs. Then the Paint Shop Pro 6 animation shop was used to piece the images together and create an avi. > > -------------------------------------------------------------------------------------------------- > > Here is the replies that I received for which I am very grateful. ... -- Hi! I'm a .signature virus! Copy me into your ~/.signature, please! -- From chemistry-request@server.ccl.net Sat Jul 22 14:42:58 2000 Received: from mail2.doit.wisc.edu (mail2.doit.wisc.edu [144.92.9.41]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA22286 for ; Sat, 22 Jul 2000 14:42:57 -0400 Received: from [128.104.71.134] by mail2.doit.wisc.edu id NAA38648 (8.9.1/50); Sat, 22 Jul 2000 13:42:58 -0500 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Message-Id: Date: Sat, 22 Jul 2000 13:42:39 -0500 To: chemistry@ccl.net From: Steven Feldgus Subject: Re: G98 ONIOM and TM We've been doing a lot of ONIOM(B3LYP:HF:UFF) jobs on a transition metal complex, and from our experience, we've found that the Gaussian UFF routines are not tremendously robust. I sent Gaussian several emails in late 1998 telling them of what we found, but never got any response. We needed to add several UFF atom types into the UFF code (in the utilam.f and utilnz.f files) in order for UFF to handle square planar rhodium complexes and coordinated olefins. The potential for linear bonds, like -CN, was also wrong (there was a maximum at 180). More recently, we've found that the ordering of the first few atoms can make a HUGE difference in whether UFF has a prayer of handling the molecule. Virtually everything in our molecule is within three bonds of rhodium, but we zeroed out what torsions we could. Having proper connectivity was critical for getting our systems to work. Steve Feldgus Dept. of Chemistry University of Wisconsin-Madison From chemistry-request@server.ccl.net Sat Jul 22 14:39:52 2000 Received: from tigre.ucb.br (tigre.ucb.br [200.236.72.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA22266 for ; Sat, 22 Jul 2000 14:39:37 -0400 Received: from prg-quimica-02 (country.ucb.br [200.236.72.12]) by tigre.ucb.br (AIX4.3/UCB 8.8.8/8.8.8-DM) with SMTP id QAA16552; Sat, 22 Jul 2000 16:39:49 -0200 Message-ID: <001e01bff406$5a16fba0$02aa000a@prg-quimica-02.ucb.br> From: "Carlos Frederico" To: Subject: problems with G98W Date: Sat, 22 Jul 2000 14:57:50 -0300 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_001B_01BFF3ED.34C9C3A0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 This is a multi-part message in MIME format. ------=_NextPart_000_001B_01BFF3ED.34C9C3A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable hi all. Recently, i bought Gaussian 98 for Windows, version A.9. I=B4m doing some CBS-APNO calculations on ethanol (CH3CH2OH), but = seems to be a problem. I got a 750 MHz, 384 MB RAM, 29 Gb HD, Windows 98 box. But in the 4th step (Geom=3DAllCheck Guess=3DTCheck = QCISD(T)/6-311++G(2df,p)) the job stop and the output file comes with = the word writwa ending it. It=B4s not as my HD was full, still got 12Gb available. Check out an extract from my output file below. I changed the size of the RWF files and the RAM available to G98W, = but nothing seems to work. Anyone of you guys came across such a problem? How can i solve it? Perhaps if i change my OS to Windows NT, will it solve my problem? Or is there any kind of hardware incompatibiliy with G98W? It=B4s good to remember that jobs with smaller molecules, like H2O, = ended ok. Thanks for any help. Bye, Fred ********************************************* Gaussian 98: x86-Win32-G98RevA.9 19-Apr-2000 28-Jun-2000 ********************************************* %RWF=3D1,1500MB,2,1500MB,3,1500MB,4,1500MB,5,1500MB,6,1500MB %nosave %Mem=3D70MB %Chk=3Detanol_cbs Default route: MaxDisk=3D13GB ------------------------------------------------------ #P Geom=3DAllCheck Guess=3DTCheck QCISD(T)/6-311++G(2df,p) and the result still have the error as you can see in the end of the = output file: **** Warning!!: The largest alpha MO coefficient is 0.38946032D+02 Leave Link 801 at Wed Jun 28 21:39:17 2000, MaxMem=3D 9175040 cpu: 0.0 (Enter C:\G98W\l804.exe) Closed-shell transformation, MDV=3D 9175040 ITran=3D7 ISComp=3D2. Estimate disk for full transformation 316042086 words. Semi-Direct transformation. ModeAB=3D 4 MOrb=3D 141 LenV=3D 8644168 LASXX=3D 43839164 LTotXX=3D 62693739 LenRXX=3D 69573285 LTotAB=3D 6879546 MaxLAS=3D 110060934 LenRXY=3D 0 NonZer=3D 94557874 LenScr=3D 150480979 LnRSAI=3D 218571714 LnScr1=3D 336501739 MaxDsk=3D 1744830464 Total=3D 775127717 SrtSym=3D T ITran=3D 5 JobTyp=3D0 Pass 1: I=3D 1 to 141. Complete sort for first half transformation. writwa ------=_NextPart_000_001B_01BFF3ED.34C9C3A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
hi all.
    Recently, i = bought Gaussian=20 98 for Windows, version A.9.
    I´m doing = some CBS-APNO=20 calculations on ethanol (CH3CH2OH), but seems to be a = problem.
    I got a 750 MHz, = 384 MB RAM,=20 29 Gb HD, Windows 98 box.
    But in=20 the 4th step (Geom=3DAllCheck Guess=3DTCheck QCISD(T)/6-311++G(2df,p)) = the job stop=20 and the output file comes with the word writwa ending=20 it.
   =20 It´s not as my HD was full, still got 12Gb available.
    Check out an = extract from my=20 output file below.
    I changed the = size of the RWF=20 files and the RAM available to G98W, but nothing seems to = work.
    Anyone of=20 you guys came across such a problem?
   =20 How can i solve it?
    Perhaps if i = change my OS to=20 Windows NT, will it solve my problem?
    Or is there any = kind of=20 hardware incompatibiliy with G98W?
    It´s good = to remember=20 that jobs with smaller molecules, like H2O, ended ok.
    Thanks for any=20 help.
    Bye, = Fred
 
*********************************************
Gaussian = 98: =20 x86-Win32-G98RevA.9=20 19-Apr-2000
         &nbs= p;       =20 28-Jun-2000
*********************************************
%RWF=3D1,= 1500MB,2,1500MB,3,1500MB,4,1500MB,5,1500MB,6,1500MB
%nosave
%Mem=3D= 70MB
%Chk=3Detanol_cbs
Default=20 route: =20 MaxDisk=3D13GB
------------------------------------------------------<= BR>#P=20 Geom=3DAllCheck Guess=3DTCheck QCISD(T)/6-311++G(2df,p)

and the = result still=20 have the error as you can see in the end of the = output
file:

****=20 Warning!!: The largest alpha MO coefficient is  = 0.38946032D+02

Leave=20 Link  801 at Wed Jun 28 21:39:17 2000, MaxMem=3D    = 9175040=20 cpu:
0.0
(Enter C:\G98W\l804.exe)
Closed-shell transformation,=20 MDV=3D     9175040 ITran=3D7 ISComp=3D2.
Estimate = disk for full=20 transformation   316042086 words.
Semi-Direct=20 transformation.
ModeAB=3D       &nb= sp;  =20 4 MOrb=3D           = 141=20 LenV=3D      =20 8644168
LASXX=3D     43839164 = LTotXX=3D   =20 62693739 LenRXX=3D    = 69573285
LTotAB=3D    =20 6879546 MaxLAS=3D   110060934=20 LenRXY=3D          =20 0
NonZer=3D    94557874 LenScr=3D   = 150480979=20 LnRSAI=3D   218571714
LnScr1=3D   336501739 = MaxDsk=3D =20 1744830464 Total=3D   =20 775127717
SrtSym=3D        &nb= sp; =20 T = ITran=3D           = ;=20 5
JobTyp=3D0 Pass  1:  I=3D   1 to = 141.
Complete sort for=20 first half transformation.
writwa
------=_NextPart_000_001B_01BFF3ED.34C9C3A0-- From chemistry-request@server.ccl.net Sat Jul 22 21:51:56 2000 Received: from freon.chem.swin.edu.au (freon.chem.swin.edu.au [136.186.11.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA24575 for ; Sat, 22 Jul 2000 21:51:54 -0400 Received: from localhost (marg@localhost) by freon.chem.swin.edu.au (8.9.3/8.9.3) with ESMTP id NAA204748 for ; Sun, 23 Jul 2000 13:00:41 -1300 (EST) Date: Sun, 23 Jul 2000 13:00:41 -1300 From: Margaret Wong To: CHEMISTRY@ccl.net Subject: image reconstrution Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLer's This is a somewhat off topic request but hope someone has been down this track before. I have been doing some collaborative research with a group of physicists and have a large number of multi-tiff format images which I would like to do a 3-D reconstruction from. They use a commercial package which I can not use on-site so would like to have an easier way to look at the data than traipsing off for the day. Can you recommend any packages which I can compile and run under either linux or on a SGI or a low cost package for NT windows. I have looked at the medical image FAQ which lists a large number of programs but it is hard to tell which program would be best. THANKS Regards Margaret _ Dr Margaret Wong v marg@freon.chem.swin.edu.au _-_|\ \_ (_)o Chemistry Dept ) ( mgw@swin.edu.au / \