Hi Carsten, You can always add it to the Feature Request tracker: https://sourceforge.net/tracker/?group_id=4546&atid=354546.
Cheers, -- Jason On Fri, Jun 17, 2011 at 12:24 PM, Schubert, Carsten [PRDUS] <cschu...@its.jnj.com> wrote: > 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 >> 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 > > -- 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. 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