Faiza– If what you're actually interested in is a model for the structure of the human dimeric Phenylalanine-4-hydroxylase, I suggest that rather than building it in pymol you use one from the protein model portal: http://www.proteinmodelportal.org/query/up/P00439
If you want to make such a model yourself in pymol, it is basically just a matter of aligning a copy of 1phz onto each chain from the 1j8u biological assembly. Just load 1phz twice, and align each copy to one chain of the flattened 1j8u BA. fetch 1j8u, type=pdb1 fetch 1phz create 1phz_2, 1phz flatten_obj 1j8u_ba, 1j8u align 1phz, /1j8u_ba//A align 1phz_2, /1j8u_ba//B Of course, the interface will not be optimized with this method and could lead to clashes. -Spencer P.S. Please reply to questions on the mailing list rather than directly. On Mon, Nov 2, 2015 at 7:45 AM, faiza iftikhar <faizaaiftik...@hotmail.com> wrote: > Hi Spencer, > > I didn't get my desired structure. I am new to pymol and what I want to do > is to create a dimer containing N-terminal of 1phz and 1j8u. > > Regards, > Faiza > > ------------------------------ > From: spencer.bli...@gmail.com > Date: Fri, 30 Oct 2015 15:26:16 +0100 > Subject: Re: [PyMOL] Biological assembly unit > To: faizaaiftik...@hotmail.com > CC: pymol-users@lists.sourceforge.net > > > Dealing with multi-state models is tricky. I wrote a flatten_obj > <http://pymolwiki.org/index.php/Flatten_obj> script to combine the > multiple states into a single object. (Thanks for the motivation to finally > upload my script to the wiki!) This allows you to use the normal > align/super/cealign commands to superimpose them as expected. Your example: > > run flatten_obj.py > fetch 1phz 1j8u, type=pdb1 > flatten_obj 1j8u_ba, 1j8u > flatten_obj 1phz_ba, 1phz > cealign /1phz_ba//A, /1j8u_ba//A > > Note that the dimer interface shifts somewhat between the two structures, > so it may be preferable to superimpose two copies of the 1ju8 asymmetric > unit onto both chains of 1phz_ba (or vice versa, depending on which > interface you consider more relevant). > > -Spencer > > On Thu, Oct 29, 2015 at 1:26 PM, faiza iftikhar < > faizaaiftik...@hotmail.com> wrote: > > Hi, > > I would like to know is there any way to combine N-terminal of 1phz > (biological assembly structure not asymmetric one) to 1j8u(biological > structure) in Pymol. > > Regards, > Faiza > > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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 > > >
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