Re: [PyMOL] dynamic bonding
Hi Jason, thanks for the hint. That works just fine. nick On Mon, Dec 14, 2009 at 11:12, Jason Vertrees wrote: > Nick, > > Interesting question. My best guess at this point is that PyMOL can't > do what you want. You can load the XYZ file into multiple distinct > objects: > >load myXYZ.xyz, multiplex=1 > > and each object will be shown with proper bonding. However, the > moment you try to combine those into one structure they retain the > bonding topology of the first structure. If you change any > intermediate state, then they all change. > > Anyone else? > > -- Jason > > -- > Jason Vertrees, PhD > > PyMOLWiki -- http://www.pymolwiki.org > > > > On Mon, Dec 14, 2009 at 11:30 AM, Nicolas Bock > wrote: > > Hello list, > > > > I have a bunch of xyz files that are along a transition path in a > molecule. > > When I load all of them into pymol and step through the individual > frames, > > pymol calculates the bonds only for the initial frame. This leads to > wrong > > bonding in subsequent frames since some atoms move quite a bit during the > > transition. How can I get "dynamic" bonding so that bonding is > recalculated > > for each frame? > > > > nick > > > > > > > -- > > Return on Information: > > Google Enterprise Search pays you back > > Get the facts. > > http://p.sf.net/sfu/google-dev2dev > > > > ___ > > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] dynamic bonding
I remember this posting from a while ago:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06885.html
which may have some clues.
--- begin ---
Whoops, my bad -- I duped the approval before seeing your repost!
Answer:
# first create a phony molecular trajectory
load $PYMOL_PATH/test/dat/pept.pdb, obj
for a in range(2,31): cmd.create("obj","obj",1,a)
unbond 5/c, 6/n
protect not ((5/c or 6/n) extend 4)
sculpt_activate obj, 30
sculpt_iterate obj, 30, 100
smooth obj, 30, 3
# then program a bond-break/re-form movie
mset 1 x30 1 -30 30 x30 30 -1
mdo 45: unbond 5/c, 6/n, quiet=1
mdo 100: bond 5/c, 6/n, quiet=1
frame 100
as sticks
orient 5-6/n+ca+c
mplay
# NOTE: only tested on PyMOL 1.2.x
Cheers,
warren
end
On Mon, Dec 14, 2009 at 1:12 PM, Jason Vertrees wrote:
> Nick,
>
> Interesting question. My best guess at this point is that PyMOL can't
> do what you want. You can load the XYZ file into multiple distinct
> objects:
>
>load myXYZ.xyz, multiplex=1
>
> and each object will be shown with proper bonding. However, the
> moment you try to combine those into one structure they retain the
> bonding topology of the first structure. If you change any
> intermediate state, then they all change.
>
> Anyone else?
>
> -- Jason
>
> --
> Jason Vertrees, PhD
>
> PyMOLWiki -- http://www.pymolwiki.org
>
>
>
> On Mon, Dec 14, 2009 at 11:30 AM, Nicolas Bock
> wrote:
> > Hello list,
> >
> > I have a bunch of xyz files that are along a transition path in a
> molecule.
> > When I load all of them into pymol and step through the individual
> frames,
> > pymol calculates the bonds only for the initial frame. This leads to
> wrong
> > bonding in subsequent frames since some atoms move quite a bit during the
> > transition. How can I get "dynamic" bonding so that bonding is
> recalculated
> > for each frame?
> >
> > nick
> >
> >
> >
> --
> > Return on Information:
> > Google Enterprise Search pays you back
> > Get the facts.
> > http://p.sf.net/sfu/google-dev2dev
> >
> > ___
> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> >
>
>
> --
> Return on Information:
> Google Enterprise Search pays you back
> Get the facts.
> http://p.sf.net/sfu/google-dev2dev
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
--
Return on Information:
Google Enterprise Search pays you back
Get the facts.
http://p.sf.net/sfu/google-dev2dev
___
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Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] dynamic bonding
Nick, Interesting question. My best guess at this point is that PyMOL can't do what you want. You can load the XYZ file into multiple distinct objects: load myXYZ.xyz, multiplex=1 and each object will be shown with proper bonding. However, the moment you try to combine those into one structure they retain the bonding topology of the first structure. If you change any intermediate state, then they all change. Anyone else? -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Mon, Dec 14, 2009 at 11:30 AM, Nicolas Bock wrote: > Hello list, > > I have a bunch of xyz files that are along a transition path in a molecule. > When I load all of them into pymol and step through the individual frames, > pymol calculates the bonds only for the initial frame. This leads to wrong > bonding in subsequent frames since some atoms move quite a bit during the > transition. How can I get "dynamic" bonding so that bonding is recalculated > for each frame? > > nick > > > -- > Return on Information: > Google Enterprise Search pays you back > Get the facts. > http://p.sf.net/sfu/google-dev2dev > > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] dynamic bonding
Hi Jason, sure, I have attached the xyz file to this email. We print out forces in columns 4-6 in the xyz. I run PyMOL(TM) Molecular Graphics System, Version 1.2r1. on linux, 64-bit. Let me know if you need any additional information. Thanks, nick On Mon, Dec 14, 2009 at 10:20, Jason Vertrees wrote: > Nick, > > Can I have a copy of that xyz file? I just tried loading a multi-xyz > file here and it worked fine. What system (OS) and version of PyMOL > are you using? > > Thanks, > > -- Jason > > -- > Jason Vertrees, PhD > > PyMOLWiki -- http://www.pymolwiki.org > > > > On Mon, Dec 14, 2009 at 11:30 AM, Nicolas Bock > wrote: > > Hello list, > > > > I have a bunch of xyz files that are along a transition path in a > molecule. > > When I load all of them into pymol and step through the individual > frames, > > pymol calculates the bonds only for the initial frame. This leads to > wrong > > bonding in subsequent frames since some atoms move quite a bit during the > > transition. How can I get "dynamic" bonding so that bonding is > recalculated > > for each frame? > > > > nick > > > > > > > -- > > Return on Information: > > Google Enterprise Search pays you back > > Get the facts. > > http://p.sf.net/sfu/google-dev2dev > > > > ___ > > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > TS.xyz Description: Protein Databank data -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] dynamic bonding
Hello list, I have a bunch of xyz files that are along a transition path in a molecule. When I load all of them into pymol and step through the individual frames, pymol calculates the bonds only for the initial frame. This leads to wrong bonding in subsequent frames since some atoms move quite a bit during the transition. How can I get "dynamic" bonding so that bonding is recalculated for each frame? nick -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
