Hi James Your residue numbers must be unique, and you must do the renumbering manually. For example, if your two proteins are
obj1: chain A, residues 1-213 obj2: chain A, residues 56-99 then first renumber the residues in obj2 to be after the residues in obj1: alter obj2, resi=resi-56+213+1 now you can combine: create chimeric, obj1 or obj2 now the object "chimeric" should contain the combined molecule, with residues numbered from 1 to 257. You can export this object as a pdb file and reload it to make pymol guessing the atom connectivity. Cheers, Esben On Tue, 2012-08-14 at 13:57 +0200, James Starlight wrote: > By the way I've already tried to make such thing ussing create command > > > e.g > > create test, sele, 1, 1 # (this should produce merged chains in 1 object) > > wheere sele is the selection of all atoms from both proteins. In that > case resulted test.pdb consisted of wrong secondary structure. Also > atom number in the sequence was mixed ( e.g like abababababababab,, > where I need to obtain sequenctial order aaaaaaaabbbbbbbb ). > > What I've done wrong and how I could obtain desired sequence ? > > James > > > 2012/8/14, James Starlight <jmsstarli...@gmail.com>: > > Dear PyMol users! > > > > I want to create chimeric protein (merge the N term of the second > > protein to the C term of the first protein) from two initial pdb's. > > How I could do this for further processing of that chimeric protein > > for MD simulation ? > > > > > > Thanks for help, > > > > > > James > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > 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 > ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ 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
