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Re: [Jmol-users] animation multiple files
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From: adriano c. <adr...@un...> - 2005-11-01 22:52:42
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Hi Tim, I have downloaded the SPV and done the job, but I had to rely on the "quick fit" built in alignment because it was really impossible to do it by hand. However now I have the file I wanted and the animation in Jmol playing. It is still a bit "jumpy", and also there is no possibilty to animate the hypothetical incoming and outgoing objects, such as Ca ions, ATP, ADP etc....but I think students might like it. So, many thanks for your suggestions. Ciao Adriano Il giorno 29/ott/05, alle ore 16:55, Timothy Driscoll ha scritto: > On Oct 29, 2005, at 10:04 a, adriano ceccarelli wrote: > > >> Tim, >> many thanks. I tried and in principle it works beautifully. >> Unfortunately the models are all placed and rotated differently, >> so it would be reeeeeeeally difficult to get a smooth animation. >> Unless, of course, there are some trick I am unaware of.....:-)) >> >> > > hi Adriano, > > ah; you need to align the structures first. Jmol can not do this, > but try SwissPdbViewer or VMD. SPV can load multiple models, align > them, and export as a multiple-model file that you can then open > and animate in Jmol. I don't know much about aligning in VMD, > except that it can be done. > > best, > > tim > > > >> Il giorno 29/ott/05, alle ore 01:35, Timothy Driscoll ha scritto: >> >> >> >>> On Oct 28, 2005, at 7:17 p, adriano ceccarelli wrote: >>> >>> >>> >>> >>> >>>> Hi all, >>>> I would like to display sequentially the various states for >>>> which the Ca2+ pump has structures available ina kind of >>>> animation. I have read the archives about the possibility >>>> obtaining an animation of multiple files but I am a bit >>>> confused. How do I get a "concatenated PDB file" ? >>>> >>>> >>>> >>>> >>>> >>> >>> hi Adriano, >>> >>> pretty easy: >>> >>> 1. create a new text file. >>> 2. open one of your structure files and copy the entire contents. >>> 3. paste into the new text file from (1). >>> 4. surround with MODEL # and ENDMDL, like this: >>> >>> MODEL 1 >>> ATOM... >>> ATOM... >>> ... >>> ENDMDL >>> >>> 5. repeat steps 2-4 for each desired structure. end result: >>> >>> MODEL 1 >>> ATOM... >>> ATOM... >>> ... >>> ENDMDL >>> MODEL 2 >>> ATOM... >>> ATOM... >>> ... >>> ENDMDL >>> MODEL 3 >>> ATOM... >>> ATOM... >>> ... >>> ENDMDL >>> ... >>> >>> >>> in Jmol, each structure can now be accessed using model or (IIRC) >>> frame. see Bob Hanson's script doc for usage details (<http:// >>> www.stolaf.edu/people/hansonr/jmol/docs/>). >>> >>> >>> hope that helps! >>> >>> tim >>> -- >>> Timothy Driscoll em: mol...@ma... >>> molvisions - see. grasp. learn. ph: 919-368-2667 >>> <http://www.molvisions.com/> im: molvisions >>> usa:virginia:blacksburg tx: >>> mol...@vt... >>> >>> >>> >>> >>> >>> >>> >>> >>> ------------------------------------------------------- >>> This SF.Net email is sponsored by the JBoss Inc. >>> Get Certified Today * Register for a JBoss Training Course >>> Free Certification Exam for All Training Attendees Through End of >>> 2005 >>> Visit http://www.jboss.com/services/certification for more >>> information >>> _______________________________________________ >>> Jmol-users mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >>> >> >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by the JBoss Inc. >> Get Certified Today * Register for a JBoss Training Course >> Free Certification Exam for All Training Attendees Through End of >> 2005 >> Visit http://www.jboss.com/services/certification for more >> information >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > -- > Timothy Driscoll em: mol...@ma... > molvisions - see. grasp. learn. ph: 919-368-2667 > <http://www.molvisions.com/> im: molvisions > usa:virginia:blacksburg tx: mol...@vt... > > > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. > Get Certified Today * Register for a JBoss Training Course > Free Certification Exam for All Training Attendees Through End of 2005 > Visit http://www.jboss.com/services/certification for more information > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |