From: Adrian B. <adr...@ya...> - 2004-11-03 04:26:48
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Hi Miguel, Thanks for the tip on force vectors - that sounds a very efficient way to do things - is this sort of thing possible with PDB files? Or is there a way to convert my PDB crystals into xyz ones? Perhaps an example somewhere of the force vectors and what they actually mean physically? Thanks very much, Adrian > Hi there group, > > I have just been mucking around creating scripts, and > I was wondering how you can just move *some* of the > atoms in the crystal - I tried selecting some of them > and then doing a move command but it didn"t work. What > should I be doing do you think? There are no script commands to do this type of operation. > Basically I am trying to emulate a vibration in the > crystal of just some elements ... is this even > possible? Atoms can have force vectors. You can create force vectors for specific atoms. The mechanism for doing this depends upon the file type. For xyz files just add three more floats (for a total of 6 floats per atom) which define the force vector. Then make them move using the vibration script commands. Miguel Find local movie times and trailers on Yahoo! Movies. http://au.movies.yahoo.com |
From: Adrian B. <adr...@ya...> - 2004-11-03 05:36:49
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> From: Bob Hanson <ha...@st...> Hi there Bob, > To: jmo...@li... > Subject: Re: [Jmol-users] movement of just some > atoms > > I think you have to create an animation and display > it > as a series of frames. Does > > http://www.stolaf.edu/people/hansonr/jmol/inline/ > > work for you? [third example, "Use .loadinline()"?] Yes this does work for me - is it possible to get a copy of the script so I can see how it is done? Thanks, Adrian Find local movie times and trailers on Yahoo! Movies. http://au.movies.yahoo.com |
From: Bob H. <ha...@st...> - 2004-11-03 11:09:24
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I think you just "show source" on that left-hand frame. But now that I look at it, you will probably also want to employ a couple of other tricks. If all you want to do is show two different arrangements of atoms, all you need to do is get your data in the form of that third "multiple model" .xyz format as a file, then load it as a set of models and display the frame you want. Or do you need it to be more flexible? Do you need to have some JavaScript determine on the fly what atoms to move (perhaps by user selection)? Then you need to use the .loadInline() method. In that case, you will want to preserve the orientation as well. For that you need something like what is being done in http://www.stolaf.edu/people/hansonr/jmol/docs/examples/moveto.htm with the "saveAngle()" command. Bob Adrian Brown wrote: >>From: Bob Hanson <ha...@st...> > > > Hi there Bob, > > >>To: jmo...@li... >>Subject: Re: [Jmol-users] movement of just some >>atoms >> >>I think you have to create an animation and display >>it >>as a series of frames. Does >> >>http://www.stolaf.edu/people/hansonr/jmol/inline/ >> >>work for you? [third example, "Use .loadinline()"?] > > > > Yes this does work for me - is it possible to get a > copy of the script so I can see how it is done? > > > Thanks, > > Adrian > > Find local movie times and trailers on Yahoo! Movies. > http://au.movies.yahoo.com > > > ------------------------------------------------------- > This SF.Net email is sponsored by: > Sybase ASE Linux Express Edition - download now for FREE > LinuxWorld Reader's Choice Award Winner for best database on Linux. > http://ads.osdn.com/?ad_id=5588&alloc_id=12065&op=click > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr |
From: Miguel <mi...@jm...> - 2004-11-03 12:54:23
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Adrian wrote: > Thanks for the tip on force vectors - that sounds a > very efficient way to do things - is this sort of > thing possible with PDB files? There is no mechanism to assign force vectors within .pdb files. > Or is there a way to > convert my PDB crystals into xyz ones? Not sure which tool would work best ... openbabel is one example. > Perhaps an > example somewhere of the force vectors and what they > actually mean physically? www.jmol.org/demo/vibration These force vectors are generally assigned by programs such as Gaussian/Spartan(?) They show vibration of molecules at different frequencies. If you want to move some atoms then that is one option. Miguel |