James, I can't think of a clever way at the moment, so here's a simple solution. Just create a temporary copy of the ligand from state 2 into state 1. Then, create the new object from the protein and new_ligand:
# create a new one-state ligand from state 2 of the original create new_ligand, old_ligand, 1, 2 # create the new_obj from create new_obj, (new_ligand or protein), 1, 1 The object, new_obj, will have the ligand and protein both, now, in state 1. Alternatively, you load the multi-state structure using the multiplex flag and use create on the new objects: load some_file.pdb, multiplex=1 create new_obj, (some_file1 or some_file2) Cheers, -- Jason On Wed, Jul 18, 2012 at 12:57 PM, James Starlight <jmsstarli...@gmail.com> wrote: > Dear all! > > > I have input multi state structure consisted of protein in one state > and ligand in the second state generated by Chimera. I want to merge > both of that objects in one common object. How I could do it? > > > James > > 2012/7/18 James Starlight <jmsstarli...@gmail.com>: >> Dear all! >> >> >> I have input multi state structure consisted of protein in one state >> and ligand in the second state generated by Chimera. I want to merge >> both of that objects in one common object. How I could do it? >> >> >> James >> >> 2012/4/30 Thomas Holder <spel...@users.sourceforge.net>: >>> Hi James and Joel, >>> >>> I would use a homology modeling tool to add missing atoms (basically rebuild >>> the structure, given the incomplete structure as template). >>> >>> Examples for web servers: >>> * http://toolkit.tuebingen.mpg.de/modeller >>> * http://swissmodel.expasy.org/ >>> >>> pdb2pqr can also add a limited number of missing atoms, see >>> http://www.poissonboltzmann.org/pdb2pqr/d/web-servers >>> >>> >>> Hope that helps. >>> >>> Cheers, >>> Thomas >>> >>> Joel Tyndall wrote, On 04/30/12 00:07: >>> >>>> Surely you could use pymol mutagenesis wizard to do tis. >>>> >>>> Also James, It is a good practice to start a new thread (new email with >>>> new subject for each set of questions you have >>>> >>>> Regards >>>> >>>> Joel >>>> >>>> From: James Starlight [mailto:jmsstarli...@gmail.com] >>>> Sent: Friday, 27 April 2012 8:25 p.m. >>>> To: pymol-users >>>> Subject: Re: [PyMOL] Editing of the pdb structure >>>> >>>> Dear all! >>>> >>>> I want to prepare my pdb structure for MD simulation. I've done all >>>> required things but my protein consist of some missing heavy atoms the list >>>> of which I've obtained from my pdb hedader >>>> >>>> REMARK 470 M RES CSSEQI ATOMS >>>> REMARK 470 ARG A 220 CG CD NE CZ NH1 NH2 >>>> REMARK 470 ARG A 222 CG CD NE CZ NH1 NH2 >>>> REMARK 470 ASN B 212 O CG OD1 ND2 >>>> REMARK 470 LYS C 43 CG CD CE NZ >>>> REMARK 470 GLY C 225 O >>>> I've heard that there are some web servers wich could be usefull to build >>>> such missing atoms. >>>> In particular in my structure there are lack not only side chain atoms but >>>> also two backbone Oxygens in the Gly and Asn wich could be the main problem >>>> of such task. >>>> >>>> In any case I'll be very thankfull if you provide me with such server >>>> James >>> >>> >>> -- >>> Thomas Holder >>> MPI for Developmental Biology >>> Spemannstr. 35 >>> D-72076 Tübingen > > ------------------------------------------------------------------------------ > 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ 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
