Hi Tsjerk, My protein is a tetramer, I did some modification in the monomer and I used the transformation matrix available in the biological unit to generate the tetramer back. For this process I used the symexp option in pymol. Its working fine. I wonder the way I am doing is scientifically correct or not.
I eager to see your comments. sincerely -- Nagarajan.P Tsjerk Wassenaar wrote: $ Hi Nagarajan, $ $ I'm not sure whether this is the best way to get what you need. symexp is $ intended to regain the crystallographic symmetry, but it seem to me you $ want $ to have the biological unit. The pdb files in the RCSB PDB are usually $ also $ available as biological unit and it should be possible to retrieve these $ automatically. Alternatively, the pdb file usually contains information $ about the transformations involved to get the symmetry related mates in $ the $ biological unit. This does not need to correspond to the crystal symmetry $ which Pymol uses for symexp. $ $ But these are just my two cents... $ $ Tsjerk $ $ On 11/3/07, Nagarajan <[email protected]> wrote: $> $> Hello all, $> $> Thanks. I found the way to do that. $> $> symexp sym, test_2(test_2),4.0 ====> to generate symmetry $> $> sincerely $> -- $> Nagarajan.P | Junior Research Fellow $> Computational Protein Science Research Group $> NCBS | TIFR $> Bangalore | India $> $> Nagarajan wrote: $> $ Hello All, $> $ $> $ I am having 2 queries $> $ $> $ 1. I like to know the command line argument to use the generate $> symmetry $> $ option. $> $ $> $ 2. I like to do this for around 400 morphs. All the morphs are $> monomer, $> I $> $ need to generate their tetramer. I am having the transition matrix. I $> like $> $ to write a code to do this. $> $ $> $ Please help me to do this. $> $ Thanks in advace $> $ $> $ Sincerely $> $ -- $> $ Nagarajan.P | Junior Research Fellow $> $ Computational Protein Science Research Group $> $ NCBS | TIFR $> $ Bangalore | India $> $ $> $ $> $ $> $> $> $> ------------------------------------------------------------------------- $> This SF.net email is sponsored by: Splunk Inc. $> Still grepping through log files to find problems? Stop. $> Now Search log events and configuration files using AJAX and a browser. $> Download your FREE copy of Splunk now >> http://get.splunk.com/ $> _______________________________________________ $> PyMOL-users mailing list $> [email protected] $> https://lists.sourceforge.net/lists/listinfo/pymol-users $> $ $ $ $ -- $ Tsjerk A. Wassenaar, Ph.D. $ Junior UD (post-doc) $ Biomolecular NMR, Bijvoet Center $ Utrecht University $ Padualaan 8 $ 3584 CH Utrecht $ The Netherlands $ P: +31-30-2539931 $ F: +31-30-2537623 $
