Right. It has limited applications. I'm not sure I'm really very keen on
that animation you have there, though...
On Tue, Sep 22, 2009 at 3:10 PM, Eric Martz <[email protected]>wrote:
> Dear Bob,
>
> Thanks for reminding me that I should be using "load trajectory" for
> multiple-model PDB files where only the coordinates change, not the
> atoms. I note that only one frame can be displayed at a time in
> trajectory mode. Often I want to show a ligand from the docked frame
> in other frames, e.g. the morph of tamiflu binding to neuraminidase 1
> by induced fit:
>
> http://proteopedia.org/wiki/index.php/Avian_Influenza_Neuraminidase%2C_Tamiflu_and_Relenza#Tamiflu_Binds_to_N1_by_Induced_Fit
>
> I suppose the best way to do this is to put the ligand in a separate
> PDB file and load it separately. I haven't tried all this yet.
>
> -Eric
>
> At 9/20/09, Robert Hanson wrote:
> >Eric -- a thought comes to mind. Have you tried "load trajectory"? It
> >saves hugely on memory and should make animations run faster as well.
> >In your case then there are only 1996 atoms. Quite a savings.
> >
> >You have to use the latest build, at
> >http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip because
> >there is a bug in 11.9.4 and 11.8.5 that broke trajectories.
> >
> >Bob
> >
> >
> >On Sun, Sep 20, 2009 at 11:09 AM, Eric Martz
> ><[email protected]> wrote:
> > > I found a two-command sequence that freezes Jmol application. I
> > > report it in case it would be desirable to handle this error in a
> > > more graceful manner.
> > >
> > > Tests were with Jmol application 11.9.4, under OS 10.5.8 (current
> > > Leopard), with java 1.5.0_20 (current Apple).
> > >
> > > While typing commands, I inadvertantly gave a pdb filename in a
> > > script command. After some experimentation, I found that this 2
> > > command sequence reproducibly freezes Jmol (cannot rotate model with
> > > mouse, cannot type commands, cannot raise menu, cannot quit; forced
> quit).
> > >
> > > $ script hivdrug.pdb # note .pdb, not .spt
> > > $ exit
> > >
> > >
> > >
> >
> ------------------------------------------------------------------------------
> > > Come build with us! The BlackBerry® Developer Conference in SF, CA
> > > is the only developer event you need to attend this year. Jumpstart
> your
> > > developing skills, take BlackBerry mobile applications to market and
> stay
> > > ahead of the curve. Join us from November 9-12, 2009. Register
> now!
> > > http://p.sf.net/sfu/devconf
> > > _______________________________________________
> > > Jmol-users mailing list
> > > [email protected]
> > > https://lists.sourceforge.net/lists/listinfo/jmol-users
> > >
> >
> >
> >
> >--
> >Robert M. Hanson
> >Professor of Chemistry
> >St. Olaf College
> >1520 St. Olaf Ave.
> >Northfield, MN 55057
> >http://www.stolaf.edu/people/hansonr
> >phone: 507-786-3107
> >
> >
> >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
> >
>
> >------------------------------------------------------------------------------
> >Come build with us! The BlackBerry® Developer Conference in SF, CA
> >is the only developer event you need to attend this year. Jumpstart your
> >developing skills, take BlackBerry mobile applications to market and stay
> >ahead of the curve. Join us from November 9-12, 2009. Register
> now!
> >http://p.sf.net/sfu/devconf
> >_______________________________________________
> >Jmol-users mailing list
> >[email protected]
> >https://lists.sourceforge.net/lists/listinfo/jmol-users
>
> /* - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Eric Martz, Professor Emeritus, Dept Microbiology
> U Mass, Amherst -- http://Martz.MolviZ.Org
>
> Top Five 3D MolVis Technologies http://Top5.MolviZ.Org
> 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org
> Biochem 3D Education Resources http://MolviZ.org
> See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
> ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
> Atlas of Macromolecules: http://atlas.molviz.org
> Workshops: http://workshops.molviz.org
> World Index of Molecular Visualization Resources: http://molvisindex.org
> PDB Lite Macromolecule Finder: http://pdblite.org
> Molecular Visualization EMail List (molvis-list): http://list.molviz.org
> Protein Explorer - 3D Visualization: http://proteinexplorer.org
> - - - - - - - - - - - - - - - - - - - - - - - - - - - */
>
>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry® Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9-12, 2009. Register now!
> http://p.sf.net/sfu/devconf
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
------------------------------------------------------------------------------
Come build with us! The BlackBerry® Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9-12, 2009. Register now!
http://p.sf.net/sfu/devconf
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
