> Hi Everyone, > > I have been trying to build a virus capsid using pymol. The biological unit > for the complete structure is not available. :( > > My first attempt at getting this done was by using the ?rotate? and > ?translate? commands. Unfortunately, these commands can only move objects > either relative to the main axes or the viewer?s position (not relative to > existing objects), thus I had to calculate the rotation angles and > translation angle/distances for every single object (not practical). > > I have been advised to try the ?supercell.py? script. Is supercell the right > tool for the job? Any advice would be much appreciated. > > Marcelo
Dear Marcelo The subunits in a virus capsid are related by non-crystallographic symmetry, therefore the crystallographic symmetry operations accessed by supercell are not sufficient to generate the capsid. Structures derived from cryoEM do no contain meaningful crystallographic symmetry information, the crystallographic symmetry record in the PDB file is set to a generic CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 The symmetry operations needed to generate the full capsid are given by the BIOMT transformations in the header of the pdb file. If this information is not given in the header, the pdb cannot generate the full capsid To see all subunits in the biological unit, you need to specify "set all_states, on” (e.g. adenovirus structure 3IYN) The Virus Particle Explorer Database VIPERdb (http://viperdb.scripps.edu) offers a comprehensive collection of virus structures and a server to generate pdb files for full and partial virus capsids: http://viperdb.scripps.edu/oligomer_multi.php best regards Annemarie ------------------------------------------------------------------------------ BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF _______________________________________________ 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
