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Re: crystal structures with Chime
by Mitch Miller 06 Mar '97

06 Mar '97

Hello Richard, I think you could work around the problem my coding <embed src="mycrystal.xyz" display3D="ball&stick" height=300 width=300...> This way the structure would initially appear in ball and stick mode. If you have any structures on the Web, I'd be glad to verify this approach for you. Mitch At 12:29 AM 3/6/97 -0800, RICHARD SINGER wrote: >You may have encountered the following problem when using Chime > - when viewing structure files in the XYZ format one is >typically offered a blank screen. The reason is that the default >display mode is "stick" mode. XYZ files have no connectivity >information so no bonds are drawn if the lattice parameter is larger >than the threshold value beyond which Chime assumes atoms cannot >bond. Of course the structure appears if you change to "ball and >stick" but this might not occur to the uninitiated who would assume >something was wrong with the structure file. >Is there a way round this problem? > >Richard Singer Mitchell Miller MDL Information Systems, Inc. (801) 569-1390 VoiceMail (800)955-0051 ext. 2163 mitch(a)mdli.com ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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marking paperless submissions of work
by RICHARD SINGER 06 Mar '97

06 Mar '97

In reply to Jeffrey Nauss who asked about marking paperless submissions of coursework there's no essential difference in marking sumbitted coursework on paper or in an electronic document. As I stated earlier I favour email submission of work as wordprocessor or spreadsheet file attachments to email. These files can be extracted, read and edited to include the marker's comments (in red of course!). The edited file is then returned to the sender by email so turnround can be very fast. Richard Singer ----------------------------------------- Dr Richard Singer School of Applied Chemistry Kingston University Penrhyn Road Surrey KT1 2EE UK Tel 0181 547 2000 ext 2471 FAX 0181 547 7562 ----------------------------------------- ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Re: paperless submission os Student Cousework
by Jeffrey.Nauss＠UC.Edu 06 Mar '97

06 Mar '97

On Mar 6, 8:47am, RICHARD SINGER wrote: > Having said that the marking and return of the work was the quickest > ever and I have repeated the exercise with better instructions with > more success. How does one "mark" paperless assignments? An honest question... -- Jeffrey L. Nauss, PhD Telephone: 513-556-0148 Dir. Molec. Model. Serv. Fax: 513-556-9239 Department of Chemistry e-mail: Jeffrey.Nauss(a)UC.Edu University of Cincinnati URL http://www.che.uc.edu/~nauss ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Paperless submission
by Dr Mary Masson 06 Mar '97

06 Mar '97

Further to Richard Singer's comments, I have been collecting work on discs for years, and I did have a spate of viruses one year. Now students are told that they will lose a significant number of marks if I find any viruses - so they have all learned to use the virus-checkers. I still virus-check all the discs before going any further, but they have all been clean since I said marks would be lost. ---------------------- Dr Mary Masson Department of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen AB24 3UE Tel. 01224 272931 m.masson(a)abdn.ac.uk ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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paperless submission os Student Cousework
by RICHARD SINGER 06 Mar '97

06 Mar '97

My experience of paperless coursework submission at Kingston University has been mixed, but on the whole encouraging! I first tried it a few years ago when 60 second year students were requested to submit some spreadsheet chemistry exercises on floppy disk for marking. I detected several viruses on disks that had been prepared on students home PCs. Beware! On the plus side I was still using the uncollected disks two years later! More recently I tried Email submission of similar work from the first year diploma students. I received several blank attachments, lots of files called "task1.doc" etc which all had to be renamed as they were extracted - it was a nightmare! Having said that the marking and return of the work was the quickest ever and I have repeated the exercise with better instructions with more success. I'd say that on the whole that the advantages outweigh the disadvantages, but you really need to think about the experiment before you launch it! I won't be asking for disk submissions again. Richard Singer ----------------------------------------- Dr Richard Singer School of Applied Chemistry Kingston University Penrhyn Road Surrey KT1 2EE UK Tel 0181 547 2000 ext 2471 FAX 0181 547 7562 ----------------------------------------- ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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crystal structures with Chime
by RICHARD SINGER 06 Mar '97

06 Mar '97

You may have encountered the following problem when using Chime - when viewing structure files in the XYZ format one is typically offered a blank screen. The reason is that the default display mode is "stick" mode. XYZ files have no connectivity information so no bonds are drawn if the lattice parameter is larger than the threshold value beyond which Chime assumes atoms cannot bond. Of course the structure appears if you change to "ball and stick" but this might not occur to the uninitiated who would assume something was wrong with the structure file. Is there a way round this problem? Richard Singer ----------------------------------------- Dr Richard Singer School of Applied Chemistry Kingston University Penrhyn Road Surrey KT1 2EE UK Tel 0181 547 2000 ext 2471 FAX 0181 547 7562 ----------------------------------------- ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Re: chime {rotation speed and Chime 1.0...)
by Tim Maffett 06 Mar '97

06 Mar '97

At 05:01 PM 3/5/97 GMT, John R. Nash wrote: >(this message cc:'d to the MOTM page creator as well as sent to ChemWeb) > >Trevor Gilson <T.R.Gilson(a)soton.ac.UK> said: >>The latest motm goes round a bit too fast with chime (is this >>clock-dependent?). Must be close to the epilepsy-inducing rep rate. > >I agree that the molecule spins too quickly, and I think I may know why. >When Chime reached version 1.0, there was a change in the spinrate >parameter, such that "normal" spin rates with older chime versions now spun >a lot faster. The parameter is now "degrees per second," with a 30 degree >spin of the y axis the default. See >http://www.mdli.com/chemscape/chime/chimehelp.html#Dev2 for details. FYI, >the current MOTM page is set with SpinY=360, or one rotation per second. >When I upgraded to 1.0, I had to slow down all of my overly hyperactive >molecules.... (shameless plug: >http://www.chem.wisc.edu/~casey/research.html) > > John is correct here, Chime 1.0 was fixed so that it correctly took the spinX/Y/Z parameter into account and tried to correctly 'match' the requested degrees of rotation to watch actually occurred. Unfortunately one side-effect of this bug fix results in 'overly hyperactive' chimed structures. Chime's rotations should *not* be dependent on the clock speed of the computer. (It is possible that a slower computer would rotate a 'difficult' structure SLOWER, but never a fast computer rotating faster (then requested)). There are several factors that effect rotation: spinFPS: Frames per second that chime will try to display/apply the requested rotation parameters spinX, spinY, spinZ: The degrees per second of rotation for each axis. The degrees of rotation for each 'frame' of the rotation is computed like this: frameX = spinX/spinFPS frameY = spinY/spinFPS frameZ = spinZ/spinFPS For each 'frame' that Chime moves structures the above frameX/Y/Z amount. Chime (as of 1.0) will now try it's best to achieve the requested frame rate, it should never go *faster* then the requested frame rate. The max FPS that can be *achieved* on different machines varies, but in practice no Windows 3.1/95 machine can get more that 17 frames per second because of limitations of the timer on this platform. The SGI should be able to get up to 60 FPS, and a fast PowerMac can probably get near 60 as well. The 'move' command in Chime 1.0's scripting language can be used for a more precise control of rotation/zooms/translates. The command allows the other to specify the amount a 'move' will be 'sped up' on a users machine to compensate for a slower machine. Eric's site has some good examples, and some docs, on the move command. Hope that all made sense... -tim > ..deleted.. > >-john nash > > > >-==-John R. Nash-==-nash(a)chem.wisc.edu-==-UW-Madison Chem. Dept-==- > --- "When in doubt, roll!" --- > ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Re: chime etc
by Armel Le Bail 05 Mar '97

05 Mar '97

Trevor Gilson writes : >The latest motm goes round a bit too fast with chime (is this >clock-dependent?). Must be close to the epilepsy-inducing rep rate. >No doubt time will allow refinement of the parameters, but would it >not be better if using the mouse were to shut down the externally >induced spin? Presumably someone going in with a mouse wants to >examine still orientations. With the right button of the mouse, select "rotation stop". Rotation is useless in this case, just a demo of the power of chime in inducing epilepsy :-). I don't know if the rotation is clock-dependent, it is surely model-size and computer-power -dependent. Just another more complaint and I stop the rotation :-| Armel Le Bail, Laboratoire des Fluorures URA CNRS 449 Faculte des Sciences, Universite du Maine, F-72017 Le Mans, France http://fluo.univ-lemans.fr:8001/ and/or http://pcb4122.univ-lemans.fr/ ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Re: chime etc
by John R. Nash 05 Mar '97

05 Mar '97

(this message cc:'d to the MOTM page creator as well as sent to ChemWeb) Trevor Gilson <T.R.Gilson(a)soton.ac.UK> said: >The latest motm goes round a bit too fast with chime (is this >clock-dependent?). Must be close to the epilepsy-inducing rep rate. I agree that the molecule spins too quickly, and I think I may know why. When Chime reached version 1.0, there was a change in the spinrate parameter, such that "normal" spin rates with older chime versions now spun a lot faster. The parameter is now "degrees per second," with a 30 degree spin of the y axis the default. See http://www.mdli.com/chemscape/chime/chimehelp.html#Dev2 for details. FYI, the current MOTM page is set with SpinY=360, or one rotation per second. When I upgraded to 1.0, I had to slow down all of my overly hyperactive molecules.... (shameless plug: http://www.chem.wisc.edu/~casey/research.html) >No doubt time will allow refinement of the parameters, but would it >not be better if using the mouse were to shut down the externally >induced spin? Presumably someone going in with a mouse wants to >examine still orientations. Well, it is simple to turn off the rotation using the popup menu, and IMHO it it useful to be able to "tweak" a rotating molecule with the mouse to adjust its spinning orientation. Your mileage may vary, of course... -john nash -==-John R. Nash-==-nash(a)chem.wisc.edu-==-UW-Madison Chem. Dept-==- --- "When in doubt, roll!" --- ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Paperless Submission of Student Projects/Coursework
by Rzepa, Henry 05 Mar '97

05 Mar '97

For the first time this year, we have operated a "paperless" undergraduate course, and the results seeming sufficiently interesting to post here The course was Chemical IT, http://www.ch.ic.ac.uk/local/it/ and assessment was by course project. 15 topics were suggested, and students had to select one and notify us of their selection by e-mail They were given 2 months to complete the project; access to computers being during the free time from lectures, tutorials etc.Because there was no printing requirement, the usual last minute rush to use overheated (and in our case broken) printers with no paper or ink cartridges did not occur. Around 70 projects were submited, which represents a high completion rate, of which 2 actually were on paper, around 50 on floppy disk, and about 20 as e-mail enclosures. One was "received" as a URL pointer to a private Web page from an Internet service provider (ie it did not actually reside on campus at all!) Around 50 projects were in word processor format, and 20 were in HTML + images. Several of the better ones can be seen on http://www.ch.ic.ac.uk/local/projects/ Assesment was on-screen, and the use of good indexing and structuring by many students made this process rapid and quick. We were not able to cover the scripts however with copious remarks in red ink! Overall the process seems to have motivated the students, who on average displayed docukent creation skills that many of the staff here do not have, and seems certain to be repeated on a larger scale in our dept in the future. If anyone else has any experiences to report on the paperless UG environment, do please post here. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa(a)ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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