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
> >
> > ---------------------------------------------------------------------
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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
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