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 content >> > authoring tool. Experience the power of Track Changes, Inline Image >> > Editing and ensure content is compliant with Accessibility Checking. >> > http://p.sf.net/sfu/ephox-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- >> 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 ------------------------------------------------------------------------------ EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-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
