Hi Hong, In your PDB file if the BIOMT transformation matrix (under remark 350) is provided, you can use this script to generate the biological assembly : http://watcut.uwaterloo.ca/cgi-bin/makemultimer/
Greetings, Abhi On Thu, Apr 25, 2013 at 9:31 AM, sujata halder <halder.suj...@gmail.com>wrote: > Hi, > > In continuation to the previous suggestion about using the 'Oligomer > Generator' in viperdb. To use viperdb, your pdb needs to be in the viper > format. So download any pdb (example this one : > http://viperdb.scripps.edu/cgi-bin/viper_coord.cgi?VDB=1z14) and then > superpose your monomer onto this reference viper format pdb....and then > upload your 'moved' pdb into the Oligomer generator 'browse' option. Then > select the T number and the option for 60mer, 30mer etc. > If this is an already published pdb then just input the id in the homepage > and then the next page will have options for you to download a > whole capsid or half capsid. > > -Tina > > > On Thu, Apr 25, 2013 at 2:48 AM, Bradley Kearney <bmkea...@ncsu.edu>wrote: > >> Hi Hong,**** >> >> ** ** >> >> I would recommend that you check out the services at the VIPERdb website >> http://viperdb.scripps.edu. It looks like the oligomer tool ( >> http://viperdb.scripps.edu/oligomer_multi.php) might be useful for what >> you want to do. They have many of the virus structures from the PDB already >> processed for you, or you could upload your own PDB coordinate file.**** >> >> ** ** >> >> Brad**** >> >> ** ** >> >> ---**** >> >> Bradley Kearney, Research Associate**** >> >> The Scripps Research Institute**** >> >> Department of Integrative Structural and Computational Biology**** >> >> Jack Johnson Laboratory**** >> >> ** ** >> >> ** ** >> >> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of >> *Guan Hong Hsiang >> *Sent:* Wednesday, April 24, 2013 11:19 PM >> *To:* CCP4BB@JISCMAIL.AC.UK >> *Subject:* [ccp4bb] How to generate a complete viirus PDB**** >> >> ** ** >> >> Dear all:**** >> >> I have one subunit PDB of one virus with a NCS record. Which >> program should I use to generate a complete virus PDB using the NCS? >> >> >> **** >> >> Thank you Hong Hsiang **** >> > > -- *Abhimanyu Kumar Singh *Ph.D. Student Department of Macromolecular Structures National Center for Biotechnology (CNB-CSIC) C/ Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain. E-Mail: abhimanyu.si...@cnb.csic.es
