Hi Jason,
Good to know. Could we then add this a feature request? I know Pymol is more a
'consumer' and not a 'producer' but in certain instances
this would be a nice feature to have.
Cheers,
Carsten
> -----Original Message-----
> From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com]
> Sent: Friday, June 17, 2011 11:57 AM
> To: Schubert, Carsten [PRDUS]
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Retention of ANISO Records was How to merge
> molecules in Pymol?
>
> Hi Carsten,
>
> PyMOL doesn't write non-coordinate records to disk. You'll need to
> write a script to prepend those records.
>
> Cheers,
>
> -- Jason
>
> On Fri, Jun 17, 2011 at 8:15 AM, Schubert, Carsten [PRDUS]
> <cschu...@its.jnj.com> wrote:
> > Thanks to all who replied, 'create' did the trick of combining
> multiple objects/molecules into one object quite painless. I was not
> thinking out of the box, been using create too long to slice and dice
> my molecules.
> >
> > But it turns out that I have TLS-ANISO records in my original file
> I'd like to retain, the save command does not carry them over into the
> combined file, neither are CRYST/SCALE records retained. Any flags I
> need to set?
> >
> > Cheers,
> >
> > Carsten
> >
> >> -----Original Message-----
> >> From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com]
> >> Sent: Thursday, June 16, 2011 6:14 PM
> >> To: Schubert, Carsten [PRDUS]
> >> Cc: pymol-users@lists.sourceforge.net
> >> Subject: Re: [PyMOL] How to merge molecules in Pymol?
> >>
> >> Hi Carsten,
> >>
> >> > Is there an (un)documented way of merging multiple molecular
> objects
> >> in
> >> > Pymol into one molecule, which then can be written in a nicely
> >> formatted PDB
> >> > file? I cobbled something cludgy together with 'multisave' and a
> >> couple
> >> > read-sort-save cycles, but this is ugly and probably quite
> fragile.
> >> An API
> >> > function might be much more robust. Is there a provision like this
> in
> >> > ChemPy? I've already taken care of adjusting each molecule to be
> >> unique with
> >> > respect to chain IDs and IDs, so that would not be an issue.
> >>
> >> It's documented:
> >> * help create
> >> * http://www.pymolwiki.org/index.php/Create
> >>
> >> Create can be used to create a single single-state object or a
> single
> >> multi-state object. The former will just 'do what you say' but may
> >> create biologically unrealistic molecules (it just combines the
> >> objects). The latter is better as it saves to biologically
> realistic
> >> multi-state pdbs. Try these examples:
> >>
> >> # method 1
> >> # create a single state (possibly biologically infeasible) molecule
> >> # from two objects
> >> frag ala
> >> frag cys
> >> save test.pdb, ala or cys
> >>
> >> Now load "test.pdb".
> >>
> >> # method 2
> >> # create a single multi-state object from two molecules
> >>
> >> frag ala
> >> frag cys
> >> create test, ala, 1, 1
> >> create test, cys, 1, 2
> >> save test.pdb, test, state=0
> >>
> >> Cheers,
> >>
> >> -- Jason
> >>
> >>
> >> On Thu, Jun 16, 2011 at 3:58 PM, Schubert, Carsten [PRDUS]
> >> <cschu...@its.jnj.com> wrote:
> >> > Hi,
> >> >
> >> > Is there an (un)documented way of merging multiple molecular
> objects
> >> in
> >> > Pymol into one molecule, which then can be written in a nicely
> >> formatted PDB
> >> > file? I cobbled something cludgy together with 'multisave' and a
> >> couple
> >> > read-sort-save cycles, but this is ugly and probably quite
> fragile.
> >> An API
> >> > function might be much more robust. Is there a provision like this
> in
> >> > ChemPy? I've already taken care of adjusting each molecule to be
> >> unique with
> >> > respect to chain IDs and IDs, so that would not be an issue.
> >> >
> >> > Any pointers would be appreciated.
> >> >
> >> > Cheers,
> >> >
> >> > Carsten
> >> >
> >> > ------------------------------------------------------------------
> ---
> >> ---------
> >> > EditLive Enterprise is the world's most technically advanced
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> >> > _______________________________________________
> >> > 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-
> >> us...@lists.sourceforge.net
> >> >
> >>
> >>
> >>
> >> --
> >> Jason Vertrees, PhD
> >> PyMOL Product Manager
> >> Schrodinger, LLC
> >>
> >> (e) jason.vertr...@schrodinger.com
> >> (o) +1 (603) 374-7120
> >
> >
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
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