Selam Ahmet, I cordially suggest to have a look at http://catb.org/~esr/faqs/smart-questions.html to phrase your question more effectively, such that we can provide more tailored help. It would have been nice to have an example that we could try ourselves.
I find that as preparation for MD simulations you can often get away with more casual modeling, using pymol for copy-paste. That is, provided you have a structure with the missing parts resolved, which is the case. Here is a working example, where the chains are from different models, but the principle is the same. # Get a structure with a missing loop fetch 1d0g, async=0 # Get the structure which has that loop resolved fetch 1d4v, async=0 # Extract the chain you want to fit; not really (necessary) create chainb, 1d4v and chainb # Fit the chain onto the one with the missing loop align chainb, 1d0g and chain a # Alter the chain identifier to match the target: alter chainb, chain="A" # Write the residues that are missing save missing.pdb, chainb and resi 132-144 # Now you can take the coordinates from 'missing.pdb' and insert them in the target pdb file in the right place # Remove the rubbish delete 1d4v delete chainb # Load the loop load missing.pdb # Et voila... Hope it helps, ;) Tsjerk 2011/10/14 ahmet yıldırım <ahmedo...@gmail.com>: > Thanks Michael, > > How can I overcome using Pymol? > > 14 Ekim 2011 23:05 tarihinde Michael Zimmermann <micha...@iastate.edu> > yazdı: >> >> The easiest way to model in the missing loops is to make a homology model >> of the full sequence using the incomplete structure as a template. >> (http://swissmodel.expasy.org or I-TASSER) >> >> Alternatively, you can use Modeller to model in the loop and refine it. >> >> >> >> 2011/10/14 ahmet yıldırım <ahmedo...@gmail.com> >>> >>> Dear users, >>> >>> There are 7 missing residues in xxx.pdb file. xxx.pdb consist of chain a >>> and chain b. In chain b there are only 7 missing residues. chain a is >>> complete. >>> I fitted the complete chain onto the one with missing residues, wrote the >>> new coordinates for the fitted chain and put them in the broken chain using >>> a text editor. >>> I think the chain a and chain b do not fit/overlap >>> As result, in chain b alpha is incomplete (see result image). what should >>> I do? >>> >>> 1.way: >>> pymol-file-open-protein.pdb >>> PyMOL>create chaina, chain a >>> PyMOL>align chaina and resi 2-230, chain b and resi 2-230 >>> PyMOL>save chaina.pdb, chaina >>> >>> 2.way: >>> pymol-file-open-protein.pdb >>> PyMOL>create chaina, chain a >>> PyMOL>create chainb, chain b >>> PyMOL>align chaina and resi 2-230, chainb and resi 2-230 >>> PyMOL>save chaina.pdb, chaina >>> >>> >>> Again the result didnt change :( >>> -- >>> Ahmet YILDIRIM >>> >>> >>> ------------------------------------------------------------------------------ >>> All the data continuously generated in your IT infrastructure contains a >>> definitive record of customers, application performance, security >>> threats, fraudulent activity and more. Splunk takes this data and makes >>> sense of it. Business sense. IT sense. Common sense. >>> http://p.sf.net/sfu/splunk-d2d-oct >>> _______________________________________________ >>> 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 >> >> >> >> -- >> Michael Zimmermann >> Ph.D. student in Bioinformatics and Computational Biology >> Department of Biochemistry, Biophysics and Molecular Biology >> Iowa State University > > > > -- > Ahmet YILDIRIM > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security > threats, fraudulent activity and more. Splunk takes this data and makes > sense of it. Business sense. IT sense. Common sense. > http://p.sf.net/sfu/splunk-d2d-oct > _______________________________________________ > 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct _______________________________________________ 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
