Hi Rob, Jenna, Be aware that the symmetry data (symexp) need not be equal to the biological unit transformations (remark biomt), even though it will often match.
And since I'm posting anyway, here's another possibility: load 1b8e.pdb, A create B,A alter_state 1,B,(x,y,z)=(-x,y,33.43-z) Cheers, Tsjerk On Tue, Apr 6, 2010 at 5:09 PM, Robert Campbell <robert.campb...@queensu.ca> wrote: > Hello Jenna, > > On Tue, 06 Apr 2010 00:36:38 -0400 JiangJiang Liu <jli...@uwo.ca> wrote: > >> When I open the pdb file 1B8E (a homodimer protein) through >> pymol I can only see a monomer shown in the screen. Now I know the >> biological dimer is produced through crystallographic symmetry operations >> in pymol. To generate the dimer, I think I need to convert these remark >> comands (list below) to be a readable commands by the pymol program. Does >> anyone know how to do this conversion? Or what's the commands for crystal >> symmetry operation? Thank you very much! Sincerely Jenna Liu >> >> PS: >> REMARK 350 BIOMOLECULE: >> 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: >> DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: >> A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 >> 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 >> 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 >> 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 >> 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 >> 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 >> 33.43000 > > Since the file has the crystallographic information in it, you simply have to > tell PyMOL to build the symmetry-related neighbours. You do this with the > symexp command: > > symexp <prefix>, <object>, <selection>, <cutoff> > > So if you have an object called 1b8e, you might do: > > symexp s_, 1b8e, 1b8e, 3 > > This will create new objects whose name begins with s_ and is followed by a > label that identifies the symmetry operation. You can then turn them on and > off until you find the one that is the mate of the original object. Given > the BIOMT matrix above, this will be the object that is related by a 2-fold > rotation around the crystallographic b-axis (which in this case is parallel > to the Y-axis) followed by a translation of 1/2 of the c-axis. This is the > object called "s_03-10000" in this case. > > Or as Jason has just written, fetch the biological unit directly and then > split out the states. > > Cheers, > Rob > -- > Robert L. Campbell, Ph.D. > Senior Research Associate/Adjunct Assistant Professor > Botterell Hall Rm 644 > Department of Biochemistry, Queen's University, > Kingston, ON K7L 3N6 Canada > Tel: 613-533-6821 Fax: 613-533-2497 > <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > 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 University of Groningen The Netherlands ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ 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
