Eran, excellent. Uploading now: http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_3.zip Trajectory hasn't been well tested, so perhaps you can give it a thorough test. I'd like to have this right for 11.4
What you do is load TRAJECTORY "filename" then instead of having 500 models you have one model, and instead of using MODEL or FRAME you use the TRAJECTORY command. You can only display one trajectory at a time because there is only one set of atoms, one set of bonds, one set of cartoons, etc. -- only the atom positions are changed when you change trajectories. Animation should work. The sorts of things that are probably broken are: -- popup menu probably doesn't display enough information about the trajectories -- getProperty may not provide much information or may crash Jmol -- saving and restoring the state probably won't work (I see it doesn't) -- trying to append to a trajectory hasn't been tested -- measurements may not be updated properly between trajectories -- setting animation range may be a problem -- odd behavior with cartoons and such -- ??? I'd be very interested if this solves your Java memory issue. I'm hoping it will, because it's designed to do that. That file should be there in about 10 minutes. Bob Eran Hodis wrote: >Hi Bob, > >Sounds like 'load TRAJECTORY "filename"' would help me. Actually it >might be perfect as I only need to display one model at a time. > >Is it easily fixable? > > >Best, >Eran > > >From: Bob Hanson <[EMAIL PROTECTED]> >Subject: Re: [Jmol-users] Loading several models at once >To: [email protected] >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >Eran, > >load TRAJECTORY "filename" > >is supposed to help you here. But it is currently broken, I see. What >this does is save only the atom positions for each model, not the whole >scheme. The models must have the same number of atoms; the restriction >then is that you can only display one model at a time. Would that help >you, or do you need to display multiple models? > >Bob > > > >Eran Hodis wrote: > > > > >>Hi All, >> >>I'm trying to load a multimodel PDB file into Jmol that has 30 models >>with about 5000 atoms each. >> >>It's not an issue of file format because another similar multimodel >>PDB file with 30 models but only 250 atoms each works file. >> >>Is this a memory problem and if so, what is the method for allocating >>more memory to a Jmol applet? -- I remember reading about this once >>on the mailing list but couldn't find it when searching. >> >>Thanks for the help. >> >>Best, >>Eran >> >>---------------------------------------------------------------------- >>--- >>SF.Net email is sponsored by: >>Check out the new SourceForge.net Marketplace. >>It's the best place to buy or sell services for >>just about anything Open Source. >>http://sourceforge.net/services/buy/index.php >>_______________________________________________ >>Jmol-users mailing list >>[email protected] >>https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> >> > > > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- SF.Net email is sponsored by: Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
